Dear all, I am new to FreeSurfer and I want to reproduce on 20 subjects the registration strategy as explained in Fischl paper: High-resolution inter-subject averaging and a coordinate system for the cortical surface, Fischl, B., Sereno, M.I., Tootell, R.B.H., and Dale, A.M., (1999). Human Brain Mapping, 8:272-284(1999) I found the page SurfaceRegAndTemplates - Free Surfer Wiki which is about the creation of a template for between-subject analysis but I am not sure if I have simply to use mris_make_template (in fact I do have the files spere.reg from the reconstruction step) or if I have to follow the 2-rounds procedure described in the page calling twice the make_average_subject. Which is the more correct one for my purpose? Right now, I tried with the second option but I encountered two different problems:
1. calling make_average_subject it works for 1 hour but at a certain moment it exit with errors saying that it does not find the file norm.mgz for the volume--> since I thought I was not interested in the volume registration, I tried to run the command with the --no-vol flag and in this way it works, but I am not sure this does not lead to any unpleasant consequence in the next stepsSo the command I used is:
make_average_subject --out NEW_TEMPLATE_SURFACE --subjects s1 s2 s3 ... --no-vol 2. the mris_preprocess step (after having registered the subjects obtaining sphere.reg.newtemplate files) does not work as described in the page in the link. I have to use the input --meas thickness, the hemisphere --hemi lh/rh, the output file --out preproc-lh-thicknesss-mgh and especially the target flag --target NEW_TEMPLATE SURFACE. So the whole command line is: mris_preproc --surfreg sphere.reg.newtemplate --s s1 --s s2 --s s3... --meas thickness --hemi lh --out preproc-lh-thicknesss-mgh --target NEW_TEMPLATE_SURFACE Is it correct?I get the error that it does not find the target file. For instance when it takes subject 50002_recon it says that 50002_recon/surf/lh.NEW_TEMPLATE_SURFACE.sphere.reg does not exist.And it's true because it is in the subject folder NEW_TEMPLATE_SURFACE indeed and in the subjects folder I just have lh.sphere.reg.newtemplate. -------------------------------------------------------------------------------sysname Linuxhostname marco-Lenovo-Yoga-2-Promachine x86_64user marcosrcsubject = 50002_reconsrcval = /home/marco/Desktop/SUBJECTS_freeSurfer/50002_recon/surf/lh.thicknesssrctype = curvtrgsubject = NEW_TEMPLATE_SURFACEtrgval = ./tmp.mris_preproc.9144/50002_recon.1.mghtrgtype = srcsurfreg = NEW_TEMPLATE_SURFACE.sphere.regtrgsurfreg = sphere.reg.newtemplatesrchemi = lhtrghemi = lhframe = 0fwhm-in = 0fwhm-out = 0label-src = lh.cortex.labellabel-trg = lh.cortex.labelOKToRevFaceOrder = 1UseDualHemi = 0Reading source surface reg /home/marco/Desktop/SUBJECTS_freeSurfer/50002_recon/surf/lh.NEW_TEMPLATE_SURFACE.sphere.regNo such file or directorymri_surf2surf: could not read surface /home/marco/Desktop/SUBJECTS_freeSurfer/50002_recon/surf/lh.NEW_TEMPLATE_SURFACE.sphere.regNo such file or directory---------------------------------------------------------------------------------------------- I decided to skip the mris_preproc phase and end the procedure of the online documentation. So I run again make_average_subject with --no-vol and with the additional option --surf-regsphere.reg.newtemplate.The result is the FINAL_TEMPLATE folder.Now, observing the mgh file in the mri subfolder called "mni305.cor.mgz", the template appears to be quite blurred. Is it the template or something else? In order to have all the subjects aligned with this final template I have to run again the registrations as in the second step, right? I apologize for the huge amount of questions, but I am a lot confused and I spent a lot of time thinking what I should do.Please, any help you could give me would be highly appreciated, even more if you are clear in the explanation. Best regards,Marco
Making a new folding atlas is not an easy task. I wrote a script to help called "make_folding_atlas". It is a very time consuming process, and the script assumes that you have access to a cluster running PBS/Torque through the pbsubmit command. If you don't have that, you could either write a script called pbsubmit that does something else or you could look at the script and pull out the elements you need.
On 2/27/17 5:27 AM, Marco Martinolli wrote:
Dear all,
I am new to FreeSurfer and I want to reproduce on 20 subjects the registration strategy as explained in Fischl paper:
High-resolution inter-subject averaging and a coordinate system for the cortical surface, Fischl, B., Sereno, M.I., Tootell, R.B.H., and Dale, A.M., (1999). Human Brain Mapping, 8:272-284(1999)
I found the page SurfaceRegAndTemplates - Free Surfer Wiki https://surfer.nmr.mgh.harvard.edu/fswiki/SurfaceRegAndTemplates which is about the creation of a template for between-subject analysis but I am not sure if I have simply to use mris_make_template (in fact I do have the files spere.reg from the reconstruction step) or if I have to follow the 2-rounds procedure described in the page calling twice the make_average_subject. Which is the more correct one for my purpose?
Right now, I tried with the second option but I encountered two different problems:
- calling make_average_subject it works for 1 hour but at a certain
moment it exit with errors saying that it does not find the file norm.mgz for the volume --> since I thought I was not interested in the volume registration, I tried to run the command with the --no-vol flag and in this way it works, but I am not sure this does not lead to any unpleasant consequence in the next steps So the command I used is:
make_average_subject --out NEW_TEMPLATE_SURFACE --subjects s1 s2 s3 ... --no-vol
- the mris_preprocess step (after having registered the subjects
obtaining sphere.reg.newtemplate files) does not work as described in the page in the link. I have to use the input --meas thickness, the hemisphere --hemi lh/rh, the output file --out preproc-lh-thicknesss-mgh and especially the target flag --target NEW_TEMPLATE SURFACE. So the whole command line is:
mris_preproc --surfreg sphere.reg.newtemplate --s s1 --s s2 --s s3... --meas thickness --hemi lh --out preproc-lh-thicknesss-mgh --target NEW_TEMPLATE_SURFACE
Is it correct? I get the error that it does not find the target file. For instance when it takes subject 50002_recon it says that 50002_recon/surf/lh.NEW_TEMPLATE_SURFACE.sphere.reg does not exist. And it's true because it is in the subject folder NEW_TEMPLATE_SURFACE indeed and in the subjects folder I just have lh.sphere.reg.newtemplate.
sysname Linux hostname marco-Lenovo-Yoga-2-Pro machine x86_64 user marco srcsubject = 50002_recon srcval = /home/marco/Desktop/SUBJECTS_freeSurfer/50002_recon/surf/lh.thickness srctype = curv trgsubject = NEW_TEMPLATE_SURFACE trgval = ./tmp.mris_preproc.9144/50002_recon.1.mgh trgtype = srcsurfreg = NEW_TEMPLATE_SURFACE.sphere.reg trgsurfreg = sphere.reg.newtemplate srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 0 label-src = lh.cortex.label label-trg = lh.cortex.label OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /home/marco/Desktop/SUBJECTS_freeSurfer/50002_recon/surf/lh.NEW_TEMPLATE_SURFACE.sphere.reg No such file or directory mri_surf2surf: could not read surface /home/marco/Desktop/SUBJECTS_freeSurfer/50002_recon/surf/lh.NEW_TEMPLATE_SURFACE.sphere.reg No such file or directory
I decided to skip the mris_preproc phase and end the procedure of the online documentation. So I run again make_average_subject with --no-vol and with the additional option --surf-reg sphere.reg.newtemplate. The result is the FINAL_TEMPLATE folder. Now, observing the mgh file in the mri subfolder called "mni305.cor.mgz", the template appears to be quite blurred. Is it the template or something else?
In order to have all the subjects aligned with this final template I have to run again the registrations as in the second step, right?
I apologize for the huge amount of questions, but I am a lot confused and I spent a lot of time thinking what I should do. Please, any help you could give me would be highly appreciated, even more if you are clear in the explanation.
Best regards, Marco
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Douglas Greve -
Marco Martinolli