help
519 Subscribers 
help > Voxel to Voxel and more
Showing 1-2 of 2 posts
Dec 13, 2011 06:12 PM | James Lee
Voxel to Voxel and more
Alfonso,
I think I have found another typo in the batch script, at line 519. I think it should be CONN_x.vvAnalyses. With this change my voxel-voxel second-level results script works.
Two general questions:
Is it possible to specify functional images of two sessions with the batch.Setup.spmfiles command, if the two sessions were analyzed singly? i.e. each session for each subject would have its own SPM.mat file?
Also, If I have previously run a batch setup script, and then later load the conn.mat file and press 'done', the software seems to want to do the setup all over again. I don't know how to tell it to move on to the next step.
Finally, after I use a batch setup script and then use the gui for voxel-voxel processing, I get an error when I press the second-level results button. The error is:
>> 'gui_results'
??? Error using ==> and
Matrix dimensions must agree.
Error in ==> conn at 1824
okstate=CONN_x.Setup.steps&okstate;
Error in ==> conn_menumanager at 116
feval(MM.MENU{n0}.callback{n1}{1},MM.MENU{n0}.callback{n1}{2:end});
??? Error using ==> conn_menumanager('cursorup');
Error using ==> and
Matrix dimensions must agree.
??? Error while evaluating figure WindowButtonUpFcnSince it references Setup.steps, I include below my batch setup script, in case it might be helpful. My matlab version is 7.4.0.287.Very Many Thanks!Jimclear batch;batch.filename = '/Users/jim/projects/merit/bill18/conn/testset';batch.Setup.RT = 2.08;batch.Setup.isnew=1;batch.Setup.nsubjects=18;batch.Setup.spmfiles=unip;batch.Setup.structurals = unips;batch.Setup.analyses = [3]; % for voxel to voxel analysesbatch.Setup.voxelmask = 1;batch.Setup.voxelresolution = 1;batch.Setup.masks.Grey.files = gray;batch.Setup.masks.White.files = white;batch.Setup.masks.CSF.files = csf;%batch.Setup.conditions - will take them from batch.setup.spmfilesbatch.Setup.covariates.names={'motion'};batch.Setup.covariates.files = mot;batch.Setup.done=1;conn_batch(batch);
I think I have found another typo in the batch script, at line 519. I think it should be CONN_x.vvAnalyses. With this change my voxel-voxel second-level results script works.
Two general questions:
Is it possible to specify functional images of two sessions with the batch.Setup.spmfiles command, if the two sessions were analyzed singly? i.e. each session for each subject would have its own SPM.mat file?
Also, If I have previously run a batch setup script, and then later load the conn.mat file and press 'done', the software seems to want to do the setup all over again. I don't know how to tell it to move on to the next step.
Finally, after I use a batch setup script and then use the gui for voxel-voxel processing, I get an error when I press the second-level results button. The error is:
>> 'gui_results'
??? Error using ==> and
Matrix dimensions must agree.
Error in ==> conn at 1824
okstate=CONN_x.Setup.steps&okstate;
Error in ==> conn_menumanager at 116
feval(MM.MENU{n0}.callback{n1}{1},MM.MENU{n0}.callback{n1}{2:end});
??? Error using ==> conn_menumanager('cursorup');
Error using ==> and
Matrix dimensions must agree.
??? Error while evaluating figure WindowButtonUpFcnSince it references Setup.steps, I include below my batch setup script, in case it might be helpful. My matlab version is 7.4.0.287.Very Many Thanks!Jimclear batch;batch.filename = '/Users/jim/projects/merit/bill18/conn/testset';batch.Setup.RT = 2.08;batch.Setup.isnew=1;batch.Setup.nsubjects=18;batch.Setup.spmfiles=unip;batch.Setup.structurals = unips;batch.Setup.analyses = [3]; % for voxel to voxel analysesbatch.Setup.voxelmask = 1;batch.Setup.voxelresolution = 1;batch.Setup.masks.Grey.files = gray;batch.Setup.masks.White.files = white;batch.Setup.masks.CSF.files = csf;%batch.Setup.conditions - will take them from batch.setup.spmfilesbatch.Setup.covariates.names={'motion'};batch.Setup.covariates.files = mot;batch.Setup.done=1;conn_batch(batch);
Dec 14, 2011 03:12 AM | Alfonso Nieto-Castanon - Boston University
RE: Voxel to Voxel and more
Hi James,
Again you are totally right about the batch script typo, thanks for finding this! (I am attaching the fixed conn_batch.m script for version conn13i, and I will incorporate this change into the next release)
Regarding your first question, I am sorry but currently only a single spm.mat file per subject can be entered when importing your experimental definitions from SPM (both through the gui or through the batch scripts). I will try to have this functionality (to include multiple SPM files per subject) added to the next release of the toolbox. In the meantime, one possible work-around would be to add each session as a separate 'subject' and then use the tricks discussed in this thread (http://www.nitrc.org/forum/forum.php?thread_id=2691&forum_id=1144) to perform the desired second-level analyses.
Regarding your second question, typically you would only press the 'Done' button when you want to (re)run some portion of the processing stream. If you have already run the setup step using batch scripts, then after loading your conn_*.mat file you can simply go to the appropriate tab (e.g. 'Preprocessing') and continue from there.
And regarding your third question, that was again a bug in the conn_batch script. The attached conn_batch.m file fixes this issue, but if you want to avoid having to re-run the batch script you can simply run the following from the command line (after loading your conn_*.mat project into the toolbox)
global CONN_x;
CONN_x.Setup.steps=CONN_x.Setup.steps(:)';
(and then save your project), and this should fix this issue.
Best
Alfonso
Originally posted by James Lee:
Again you are totally right about the batch script typo, thanks for finding this! (I am attaching the fixed conn_batch.m script for version conn13i, and I will incorporate this change into the next release)
Regarding your first question, I am sorry but currently only a single spm.mat file per subject can be entered when importing your experimental definitions from SPM (both through the gui or through the batch scripts). I will try to have this functionality (to include multiple SPM files per subject) added to the next release of the toolbox. In the meantime, one possible work-around would be to add each session as a separate 'subject' and then use the tricks discussed in this thread (http://www.nitrc.org/forum/forum.php?thread_id=2691&forum_id=1144) to perform the desired second-level analyses.
Regarding your second question, typically you would only press the 'Done' button when you want to (re)run some portion of the processing stream. If you have already run the setup step using batch scripts, then after loading your conn_*.mat file you can simply go to the appropriate tab (e.g. 'Preprocessing') and continue from there.
And regarding your third question, that was again a bug in the conn_batch script. The attached conn_batch.m file fixes this issue, but if you want to avoid having to re-run the batch script you can simply run the following from the command line (after loading your conn_*.mat project into the toolbox)
global CONN_x;
CONN_x.Setup.steps=CONN_x.Setup.steps(:)';
(and then save your project), and this should fix this issue.
Best
Alfonso
Originally posted by James Lee:
Alfonso,
I think I have found another typo in the batch script, at line 519. I think it should be CONN_x.vvAnalyses. With this change my voxel-voxel second-level results script works.
Two general questions:
Is it possible to specify functional images of two sessions with the batch.Setup.spmfiles command, if the two sessions were analyzed singly? i.e. each session for each subject would have its own SPM.mat file?
Also, If I have previously run a batch setup script, and then later load the conn.mat file and press 'done', the software seems to want to do the setup all over again. I don't know how to tell it to move on to the next step.
Finally, after I use a batch setup script and then use the gui for voxel-voxel processing, I get an error when I press the second-level results button. The error is:
>> 'gui_results'
??? Error using ==> and
Matrix dimensions must agree.
Error in ==> conn at 1824
okstate=CONN_x.Setup.steps&okstate;
Error in ==> conn_menumanager at 116
feval(MM.MENU{n0}.callback{n1}{1},MM.MENU{n0}.callback{n1}{2:end});
??? Error using ==> conn_menumanager('cursorup');
Error using ==> and
Matrix dimensions must agree.
??? Error while evaluating figure WindowButtonUpFcnSince it references Setup.steps, I include below my batch setup script, in case it might be helpful. My matlab version is 7.4.0.287.Very Many Thanks!Jimclear batch;batch.filename = '/Users/jim/projects/merit/bill18/conn/testset';batch.Setup.RT = 2.08;batch.Setup.isnew=1;batch.Setup.nsubjects=18;batch.Setup.spmfiles=unip;batch.Setup.structurals = unips;batch.Setup.analyses = [3]; % for voxel to voxel analysesbatch.Setup.voxelmask = 1;batch.Setup.voxelresolution = 1;batch.Setup.masks.Grey.files = gray;batch.Setup.masks.White.files = white;batch.Setup.masks.CSF.files = csf;%batch.Setup.conditions - will take them from batch.setup.spmfilesbatch.Setup.covariates.names={'motion'};batch.Setup.covariates.files = mot;batch.Setup.done=1;conn_batch(batch);
I think I have found another typo in the batch script, at line 519. I think it should be CONN_x.vvAnalyses. With this change my voxel-voxel second-level results script works.
Two general questions:
Is it possible to specify functional images of two sessions with the batch.Setup.spmfiles command, if the two sessions were analyzed singly? i.e. each session for each subject would have its own SPM.mat file?
Also, If I have previously run a batch setup script, and then later load the conn.mat file and press 'done', the software seems to want to do the setup all over again. I don't know how to tell it to move on to the next step.
Finally, after I use a batch setup script and then use the gui for voxel-voxel processing, I get an error when I press the second-level results button. The error is:
>> 'gui_results'
??? Error using ==> and
Matrix dimensions must agree.
Error in ==> conn at 1824
okstate=CONN_x.Setup.steps&okstate;
Error in ==> conn_menumanager at 116
feval(MM.MENU{n0}.callback{n1}{1},MM.MENU{n0}.callback{n1}{2:end});
??? Error using ==> conn_menumanager('cursorup');
Error using ==> and
Matrix dimensions must agree.
??? Error while evaluating figure WindowButtonUpFcnSince it references Setup.steps, I include below my batch setup script, in case it might be helpful. My matlab version is 7.4.0.287.Very Many Thanks!Jimclear batch;batch.filename = '/Users/jim/projects/merit/bill18/conn/testset';batch.Setup.RT = 2.08;batch.Setup.isnew=1;batch.Setup.nsubjects=18;batch.Setup.spmfiles=unip;batch.Setup.structurals = unips;batch.Setup.analyses = [3]; % for voxel to voxel analysesbatch.Setup.voxelmask = 1;batch.Setup.voxelresolution = 1;batch.Setup.masks.Grey.files = gray;batch.Setup.masks.White.files = white;batch.Setup.masks.CSF.files = csf;%batch.Setup.conditions - will take them from batch.setup.spmfilesbatch.Setup.covariates.names={'motion'};batch.Setup.covariates.files = mot;batch.Setup.done=1;conn_batch(batch);