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R: Re: R: Re: R: Re: Import FS data to FSL
by stdp82＠virgilio.it 27 Sep '13

27 Sep '13

Anastasia thank you very much! I have wrote to FSL mail list. They have uploaded a new web page of FDT. Anyway, these are the commands: mris_convert lh.white lh.white.giiecho lh.BA44.label lh.BA45.label > listOfAreas.txt label2surf -s lh.white.gii -o lh.BA44.gii -l listOfAreas.txtStefano ----Messaggio originale---- Da: ayendiki(a)nmr.mgh.harvard.edu Data: 27-set-2013 16.44 A: <stdp82(a)virgilio.it> Cc: <freesurfer(a)nmr.mgh.harvard.edu> Ogg: Re: [Freesurfer] R: Re: R: Re: Import FS data to FSL label2surf is an FSL command, so you can get a more authoritative answer on the FSL list, but I'd try one of the files in the surf/ directory, like lh.white or rh.white. On Fri, 27 Sep 2013, stdp82(a)virgilio.it wrote: > Hi list and Anastasia. > > Thank you very much. mri_annotatiion2label works fine. > > Becouse I should run this command: > > label2surf -s <surface> -o <outputsurface> -l <labels> > > -s,--surf input surface > -o,--out output surface > -l,--labels ascii list of label files > > I should provide also surface file relatively to each .label previously > created with mri_annotatiion2label. > > How can I do? > > Thanks, > > > Stefano > > > ----Messaggio originale---- > Da: ayendiki(a)nmr.mgh.harvard.edu > Data: 26-set-2013 0.57 > A: <stdp82(a)virgilio.it> > Cc: <freesurfer(a)nmr.mgh.harvard.edu> > Ogg: Re: R: Re: [Freesurfer] Import FS data to FSL > > > Try mri_annotation2label. > > On Wed, 25 Sep 2013, stdp82(a)virgilio.it wrote: > > > For FSL guide: > > > > I should transforms a group of labels into a surface > > > > Usage: > > > > label2surf -s <surface> -o <outputsurface> -l <labels> > > > > Compulsory arguments (You MUST set one or more of): > > > > -s,--surf input surface > > > > -o,--out output surface > > > > -l,--labels ascii list of label files > > > > Optional arguments (You may optionally specify one or more of): > > > > -v,--verbose switch on diagnostic messages > > > > -h,--help display this message > > > > > > but I should create a lh/rh.frontal.label and use it for label2surf. > > > > With mdi_binarize I can create .nii.gz but no .label. Is that correct? > > > > How I can do it? > > > > > > Thanks, > > > > > > Stefano > > > > > > > > > > ----Messaggio originale---- > > Da: ayendiki(a)nmr.mgh.harvard.edu > > Data: 25-set-2013 17.49 > > A: <stdp82(a)virgilio.it> > > Cc: <freesurfer(a)nmr.mgh.harvard.edu> > > Ogg: Re: [Freesurfer] Import FS data to FSL > > > > > > 1 - Yes. > > 2 - You can use mri_aparc2aseg to grow the cortical labels into the white > > matter (say, by 2mm). The file that it will produce will be a volume file, > > so then you just run mri_binarize to extract specific labels. Make sure > > you save them in nifti format for FSL. > > > > On Wed, 25 Sep 2013, stdp82(a)virgilio.it wrote: > > > > > Hi list, > > > > > > I have 2 questions, please. > > > > > > 1-The bedpostX that I have run for TRACULA could be used for PROBTRACKX > > > (FSL)? > > > > > > 2-I'd like to export cortical masks from FS to FSL. > > > > > > An option is mri_binarize but this way failed in probtrackx (fsl). > > > FSL list have advised me that I should use label2surf command to convert > > > label to surface files. > > > > > > Where could find the .label (according to FreeSurferColorLUT.txt) to > build > > > mask of frontal, parietal, motor, sensor, temporal and occipital lobes? > > > > > > Do you have other ways that you advise me? > > > > > > > > > Thanks, > > > > > > > > > Stefano > > > > > > > > > > > > > > > > > > The information in this e-mail is intended only for the person to whom it > is > > addressed. If you believe this e-mail was sent to you in error and the > > e-mail > > contains patient information, please contact the Partners Compliance > > HelpLine at > > http://www.partners.org/complianceline . If the e-mail was sent to you in > > error > > but does not contain patient information, please contact the sender and > > properly > > dispose of the e-mail. > > > > > > > > > > > > >_______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.

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Red Hat 6 and Freesurfer for CentOS4/CentOS6: different results?
by Garikoitz Lerma-Usabiaga 27 Sep '13

27 Sep '13

Hi, I have two identical Red Hat 6 boxes, to run recon-all-s. I just realized that in one of those I had freesurfer 5.3 for CentOS4 and in the other one I had freesurfer 5.3 for CentOS6. I have one experiment were subjects used boxes indistinctly. According to how the software is built, should I expect different results among them? Many thanks for your help, Gari

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Re: [Freesurfer] Tracula bval and bvec
by Anastasia Yendiki 27 Sep '13

27 Sep '13

Hi Gari - Just looked at your subject. The bottom of the brain is truncated in the DWIs. The slices stop in the middle of the angular bundle, which is why the -prior step failed in that pathway. But I expect there'd be problems with other tracts that reach that inferior, even if they didn't fail completely - corticospinal, uncinate, inferior longitudinal fasciculus. a.y On Thu, 26 Sep 2013, Garikoitz Lerma-Usabiaga wrote: > Hi Anastasia, > I was testing just with one subject and it finished the -prep part with > error. > Please find attached the trac-all.log file. > As this is a test user you will see some other invocations of trac-all. The > last build_stamp starts at row 54.500 aprox. > (just in case: I started new from de DICOMS and the dcm2nii, and I am using > the resulting .nii, .bvec and .bval, just in case I attached the dmrirc > too). > > Thanks again for your help! > Gari > > > On Thu, Sep 26, 2013 at 8:01 AM, Anastasia Yendiki > <ayendiki(a)nmr.mgh.harvard.edu> wrote: > > Hi Gari - Yes, that's your best option right now. Sorry for the > inconvenience. I'll make sure to add the option to have one > gradient file per subject in the next version. > > a.y > > On Thu, 26 Sep 2013, Garikoitz Lerma-Usabiaga wrote: > > Hi! Thanks for the fast answer. If I do: diff > id1.bvec id2.bvec > I can see some clear differences. > > I was told that in FSL I should use the bvecs and > bvals created in dcm2nii > per subject, so I understand I should do the same > now? > Do you think an option would be to script the > creation of a dmrirc file per > each subject and then launch as many trac-alls as > subjects? > > Thanks again, > Gari > > On Thursday, September 26, 2013, Anastasia Yendiki > wrote: > > Hi Gari - Sorry, right now the assumption is > that the gradient > vectors are the same for all subjects. How > different are they? > > a.y > > On Wed, 25 Sep 2013, Garikoitz Lerma-Usabiaga > wrote: > > Hi Anastasia,I am setting up the dmrirc > file to run > Tracula. I am using > Siemens Dicoms, so I did not specify any > setting for > bval and bvec, but when > trac-all -prep starts running it gives > the following > error: mv: cannot stat > > 'paths.../SubjectID/dmri/dwi_orig_flip.mghdti.bvecs': > No such file or > directory > > Ok, so I understand that our problem is > that we > don't have MGH Siemens > Dicom. > > So I used dcm2nii to convert it to .nii > files and > each conversion gives me a > SubjectID.bval and SubjectID.bvec. Every > .bval is > the same file, but every > .bvec file is a different one. > > I can edit "set dcm_list = " to include > all the > newly created .nii files, > but > > My question is: > - How can I specify every .bvec value > for every > subject? In the dmrirc file > everything I see is a "set bvecfile = " > option. > > Thank you very much, > Gari > > > > > The information in this e-mail is intended > only for the person > to whom it is > addressed. If you believe this e-mail was sent > to you in error > and the e-mail > contains patient information, please contact > the Partners > Compliance HelpLine at > http://www.partners.org/complianceline . If > the e-mail was sent > to you in error > but does not contain patient information, > please contact the > sender and properly > dispose of the e-mail. > > > > >

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R: Re: R: Re: Import FS data to FSL
by stdp82＠virgilio.it 27 Sep '13

27 Sep '13

Hi list and Anastasia. Thank you very much. mri_annotatiion2label works fine. Becouse I should run this command: label2surf -s <surface> -o <outputsurface> -l <labels> -s,--surf input surface -o,--out output surface -l,--labels ascii list of label files I should provide also surface file relatively to each .label previously created with mri_annotatiion2label. How can I do? Thanks, Stefano ----Messaggio originale---- Da: ayendiki(a)nmr.mgh.harvard.edu Data: 26-set-2013 0.57 A: <stdp82(a)virgilio.it> Cc: <freesurfer(a)nmr.mgh.harvard.edu> Ogg: Re: R: Re: [Freesurfer] Import FS data to FSL Try mri_annotation2label. On Wed, 25 Sep 2013, stdp82(a)virgilio.it wrote: > For FSL guide: > > I should transforms a group of labels into a surface > > Usage: > > label2surf -s <surface> -o <outputsurface> -l <labels> > > Compulsory arguments (You MUST set one or more of): > > -s,--surf input surface > > -o,--out output surface > > -l,--labels ascii list of label files > > Optional arguments (You may optionally specify one or more of): > > -v,--verbose switch on diagnostic messages > > -h,--help display this message > > > but I should create a lh/rh.frontal.label and use it for label2surf. > > With mdi_binarize I can create .nii.gz but no .label. Is that correct? > > How I can do it? > > > Thanks, > > > Stefano > > > > > ----Messaggio originale---- > Da: ayendiki(a)nmr.mgh.harvard.edu > Data: 25-set-2013 17.49 > A: <stdp82(a)virgilio.it> > Cc: <freesurfer(a)nmr.mgh.harvard.edu> > Ogg: Re: [Freesurfer] Import FS data to FSL > > > 1 - Yes. > 2 - You can use mri_aparc2aseg to grow the cortical labels into the white > matter (say, by 2mm). The file that it will produce will be a volume file, > so then you just run mri_binarize to extract specific labels. Make sure > you save them in nifti format for FSL. > > On Wed, 25 Sep 2013, stdp82(a)virgilio.it wrote: > > > Hi list, > > > > I have 2 questions, please. > > > > 1-The bedpostX that I have run for TRACULA could be used for PROBTRACKX > > (FSL)? > > > > 2-I'd like to export cortical masks from FS to FSL. > > > > An option is mri_binarize but this way failed in probtrackx (fsl). > > FSL list have advised me that I should use label2surf command to convert > > label to surface files. > > > > Where could find the .label (according to FreeSurferColorLUT.txt) to build > > mask of frontal, parietal, motor, sensor, temporal and occipital lobes? > > > > Do you have other ways that you advise me? > > > > > > Thanks, > > > > > > Stefano > > > > > > > > > > > The information in this e-mail is intended only for the person to whom it is > addressed. If you believe this e-mail was sent to you in error and the > e-mail > contains patient information, please contact the Partners Compliance > HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. > > > > >

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Conversion question
by pfotiad＠nmr.mgh.harvard.edu 27 Sep '13

27 Sep '13

Hi FS Community, I was wondering whether there is a way to convert a FLOAT type niftii file to an INT type niftii file. Thanks in advance! Best, Panos

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Question about talairach.m3z file
by Paul Beach 27 Sep '13

27 Sep '13

Hello Freesurfer community, I have a question about the file talairach.m3z, which is found in the mri/transforms directory of all subjects that have undergone recon-all. I am utilizing this file in an mri_convert script to resample AFNI processed T1volumes (and time-series data) to MNI space. However, I wanted to confirm *which* MNI talairach.m3z represents - it's MNI305, correct? Thanks! Paul -- Paul Beach DO/PhD candidate - Year VI Michigan State University - College of Osteopathic Medicine - Neuroscience Program - Bozoki Lab: Neurology/Radiology

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mri_volcluster question
by pfotiad＠nmr.mgh.harvard.edu 27 Sep '13

27 Sep '13

Hi FS Community, I am using the mri_volcluster command but for some reason the --sumfile shows up as an unknown flag. Is there another way to get a summary text file? (I am using FS 5.3 stable.) Thank you for your time! Best, Panos

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Reading surface features into a vector
by Joy-Loi Chepkoech 27 Sep '13

27 Sep '13

Dear FreeSurfer experts, I am looking for a way to read a subject's cortical thickness and volume, and surface area at each vertex into a vector that is readable by matlab. How should I go about doing this? Thanks, Joy-Loi

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group pcc maps for functional connectivity
by Caspar M. Schwiedrzik 27 Sep '13

27 Sep '13

Hi Freesurfer Experts, I am trying to calculate group pcc maps for resting state functional connectivity analyses. Unfortunately, the walkthrough does not cover this. I found several posts regarding this on the mailing list, but I am not sure which one is the right way to go: There is -m pcc in isxconcat-sess ( http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg30456.html) and there is also fast_glm_pcc (e.g., http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg22648.html) however, the various posts on the later functional all seem to differ in how to properly use it. This is in version 5.1. Please advise. Thanks, Caspar

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Extracting SUV values from Freesurfer ROIs
by Alexander Lebedev 27 Sep '13

27 Sep '13

*Dear Freesurfers,* I apologize if this question has already been asked somewhere - I didn't manage to find the answer in the archives. I have my T1 images processed in FS_5.3 and corresponding PET images co-registered with rawavg.nii-images in SPM (converted from mgz). Now I would like to extract standardized uptake values from the Freesurfer's ROIs (aparc.a2009s+aseg.mgz) in native space. Is there a straightforward way to do this? (preferably, in one command without creating multiple labels from the parcellation) Thank you very much in advance. *=======* *Best Regards,* *Alexander Lebedev* University of Bergen, Norway

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