Freesurfer May 2013

freesurfer@nmr.mgh.harvard.edu

174 participants
299 discussions

Re: [Freesurfer] mkbrainmask-sess
by Joseph Dien 20 May '13

20 May '13

I imagine this issue has been solved by now but just for the record I ran into a similar issue. In my case the problem turned out to be that FSL installs by default in /usr/local/fsl/bin but FSFAST was looking for it in /bin This was on OS X 10.8.2 with FSL Installer - Version 2.0.10 and Freesurfer 5.2.0. Is there some way to set up Freesurfer so it'll look in the correct directory? For now I'm copying the critical files to /bin but am hoping there is a better solution. Thanks! Joe > It could be. It uses fsl only to create a mask of the brain, so it probably does not need a full fsl install, but it might need more than you have. > doug > > On 3/25/12 7:05 AM, Kiley Seymour wrote: > Hi again, > Could this error be due to the fact that I don't have a full version > of fsl installed and configured on my ubuntu virtual machine? i.e. > does fsfast require fsl to be installed? > > Thanks > > K > > ------------------------------------------------------------------------ > *From:* Kiley Seymour <kiley_seym...(a)yahoo.com.au> > *To:* "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> > *Sent:* Friday, 23 March 2012 3:04 PM > *Subject:* mkbrainmask-sess > > Dear Freesurfers, > > I am currently trying to do some retinotopic mapping. I have been successful in running the reconstruction commands and setting everything up for the analysis, but I have run into problems when using the selxavg3-sess command. i.e. selxavg3-sess -a rtopy.self.lh -s IFEE2211 -no-preproc ( -no-preproc since I have co-registered and motion corrected my files in SPM). > I was unable to run this command as freesurfer could not find/media/sf_DATA1/RETINOTOPY/IFEE2211/bold/001/global.meanval.dat > So I ran mktemplate - sess, which was successfully completed. And then I ran mkbrainmask-sess (see below). > Any help with this would be much appreciated. > > Thanks > > Kiley > > FreeSurfer:~/data1/RETINOTOPY> mkbrainmask-sess -s IFEE2211 -d~/data1/RETINOTOPY > ------------------------------------------------ > /media/sf_DATA1/RETINOTOPY/IFEE2211 > Fri Mar 23 09:42:26 EDT 2012 > mkbrainmask -i template.nii.gz -o masks/brain.nii.gz -thresh 0.1 -ndil 1 -nerode 0 > FSLMATHS fslmaths.fsl > Scratch Dir is /tmp/mkbrainmask_7930 > /media/sf_DATA1/RETINOTOPY/IFEE2211/bold > mri_convert template.nii.gz /tmp/mkbrainmask_7930/in.nii > mri_convert template.nii.gz /tmp/mkbrainmask_7930/in.nii > $Id: mri_convert.c,v 1.179.2.1 2011/03/22 16:37:02 nicks Exp $ > reading from template.nii.gz... > TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 > i_ras = (-0.998558, -0.0534653, -0.00482299) > j_ras = (-0.0536701, 0.992375, 0.110955) > k_ras = (0.00114604, -0.111054, 0.993814) > writing to /tmp/mkbrainmask_7930/in.nii... > # ---------- Using FSL's BET to Extract Brain------------------ # > /media/sf_DATA1/RETINOTOPY/IFEE2211/bold > bet.fsl /tmp/mkbrainmask_7930/in.nii /tmp/mkbrainmask_7930/brain -m -f 0.1 > /home/virtualuser/freesurfer/bin/bet.fsl: 150: /bin/remove_ext: not found > /home/virtualuser/freesurfer/bin/bet.fsl: 151: /bin/remove_ext: not found > /home/virtualuser/freesurfer/bin/bet.fsl: 158: /bin/imtest: not found > [: 158: =: unexpected operator > /home/virtualuser/freesurfer/bin/bet.fsl: 380: /bin/bet2: not found > mri_binarize --i /tmp/mkbrainmask_7930/brain_mask.nii --min .01 --o/tmp/mkbrainmask_7930/brain_mask.nii > niiRead(): error opening file /tmp/mkbrainmask_7930/brain_mask.nii > > $Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $ > cwd /media/sf_DATA1/RETINOTOPY/IFEE2211/bold > cmdline mri_binarize --i /tmp/mkbrainmask_7930/brain_mask.nii --min .01 --o /tmp/mkbrainmask_7930/brain_mask.nii > sysname Linux > hostname FreeSurfer > machine i686 > user virtualuser > > input /tmp/mkbrainmask_7930/brain_mask.nii > frame 0 > nErode3d 0 > nErode2d 0 > output /tmp/mkbrainmask_7930/brain_mask.nii > Binarizing based on threshold > min 0.01 > max +infinity > binval 1 > binvalnot 0 > > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > _______________________________________________ > 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. -------------------------------------------------------------------------------- Joseph Dien, Senior Research Scientist University of Maryland E-mail: jdien07(a)mac.com Phone: 301-226-8848 Fax: 301-226-8811 http://joedien.com//

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shape difference in subcortical structures using FSL vertex Analysis
by M.Shakeri 20 May '13

20 May '13

Hi All, I need to do a shape analysis between the freesurfer segmentation results with manual segmentation. Does anyone know how can I use FSL Vertex Analysis (first_utils) ? Fsl Vertex Analysis input file is .bvars . Is there a documentation or guide to create this file type? Mah

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failures more frequent in one hemisphere
by Joshua Lee 20 May '13

20 May '13

Hi All, I recently ran a number of 2-yr-old brains through Freesurfer, and overall Freesurfer did well considering the age group. However, a subset (~10%) had catastrophic failures in the left termporal lobe in which parahippocampal cortex bled over into the hippocampal region. I've since added control points and am rerunning. However, what I found curious was that almost every failure was in the left hemisphere, not the right. Any ideas why that might happen? Using freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 Joshua

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Re: [Freesurfer] Tracula longitudinal "nan" values for highest probability path
by Anastasia Yendiki 20 May '13

20 May '13

Hi Vincent - If you upload the tracula dirs for this particular time point, I'll take a look. a.y On Mon, 20 May 2013, Vincent Brunsch wrote: > Hi Anastasia, > Thanks for your help! I had this issue with 4 tracts in total. I just want to > add that before rerunning dmri_pathstats not only pathstats.overall but also > pathstats.byvoxel was affected (in the latter there were no matrix entries at > all). > I found some information in the trac-all.log but not explicitly the command > line <- this was found in pathstats.overall.txt, though. > > After rerunning dmri_pathstats everything looks great now for 3 out of the 4 > tracts, YEAH! I am not sure what to do with the last one, though: Here, the > same error occurs but in cpts.map.txt no two lines are identical: > > For lh.cst: > 58 48 10 > 62 51 21 > 65 55 26 > 70 58 35 > 72 57 39 > 64 55 56 > > Would you suggest deleting randomly one time point for this tract of this > subject? Thanks! > Vincent > > > Am 5/20/2013 10:31 AM, schrieb Anastasia Yendiki: >> >> Hi Vincent - Thanks for bringing this to my attention. I can see what might >> cause this glitch (only in the longitudinal case) and I'll fix it in the >> next version. >> >> In the meantime, if you delete one of the two identical lines from >> cpts.map.txt, and then rerun the dmri_pathstats command line that you'll >> find in the trac-all.log of your subject, it should regenerate the stats >> files correctly. Sorry for the inconvenience. >> >> a.y >> >> On Fri, 17 May 2013, vbrunsch(a)nmr.mgh.harvard.edu wrote: >> >>> Dear Anastasia, >>> >>> When running the longitudinal tracula version on our 39 subjects I found >>> for some of them "nan"-values for the center_avg variables of some tracts. >>> When I have a look at the tract distribution and the highest probability >>> path, everything seems to be ok. However, when checking the control points >>> of this path, two of them are the same. Do you know how this could have >>> happened / what to do? >>> >>> E.g. control points of forceps major from a subject (cpts.map.txt), see >>> 4th and 5th control point: >>> >>> 63 20 39 >>> 67 31 39 >>> 59 43 38 >>> 52 42 38 >>> 52 42 38 >>> 43 32 38 >>> 50 19 33 >>> >>> And the respective pathstats.overall.txt: >>> Count 1500 >>> Volume 370 >>> Len_Min 62 >>> Len_Max 99 >>> Len_Avg 78.9307 >>> Len_Center 0 >>> AD_Avg 0.00155598 >>> AD_Avg_Weight 0.00158424 >>> AD_Avg_Center -nan >>> RD_Avg 0.000438439 >>> RD_Avg_Weight 0.000401328 >>> RD_Avg_Center -nan >>> MD_Avg 0.000810952 >>> MD_Avg_Weight 0.000795633 >>> MD_Avg_Center -nan >>> FA_Avg 0.662419 >>> FA_Avg_Weight 0.696257 >>> FA_Avg_Center -nan >>> >>> Thanks for your help!! :) >>> Best, >>> Vincent >>> >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer(a)nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >>> >>> >> >> > > >

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Re: [Freesurfer] Freesurfer MAC installation
by zkaufman＠nmr.mgh.harvard.edu 20 May '13

20 May '13

Flavia, You are going to have to be a little more specific in describing what you are trying to do and what exactly the problem is. You say you "cannot open the example Bert"... What does that mean? You can open it in tkmedit? What is the error? The procedure for getting the license is to go to this page (http://surfer.nmr.mgh.harvard.edu/registration.html) Fill out the form. Get the email. Copy the license content from the email into a file called ".license" (dont use the quotes). Place the .license fill in the /Application/freesurfer directory. It is a fairly simple process. If you do not have a .license file in /Application/freesurfer directory, nothing will work. So you must accomplish this first. -Zeke > Hi Zeke, > > many thanks for your answer > but I still cannot use freesurfer, I cannot open the example "Bert". > I am not sure that the license is placed because I cannot open this. Could > you please help me? > how can I do? > Which is theprocedure to put the license? > Why I cannot open this file? > HELP! > > On Fri, May 17, 2013 at 6:27 PM, Z K <zkaufman(a)nmr.mgh.harvard.edu> wrote: > >> Hello Flavia, >> >> The .license file should be placed in the /Applications/freesurfer >> directory. >> >> To load freesurfer, you must open the terminal type the following : >> >> >> setenv FREESURFER_HOME /Applications/freesurfer >> >> source $FREESURFER_HOME/SetUpFreeSurfer.sh >> >> -Zeke >> >> >> On 05/17/2013 12:49 PM, Flavia Niccolini wrote: >> > Hi >> > I am having trouble with the license file. >> > I created in Freesurfer a file named ".license" but I cannot open this >> > and copy the license. >> > where and how should I put the 3 lines license? >> > I tried to test my freesurfer installation with Bert but I got as >> answer >> > "command non found". >> > Please help >> > BW >> > Flavia >> > >> > >> > _______________________________________________ >> > Freesurfer mailing list >> > Freesurfer(a)nmr.mgh.harvard.edu >> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> > >> _______________________________________________ >> 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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Re: [Freesurfer] F Problem running : mri_cc -aseg.auto_
by Bruce Fischl 20 May '13

20 May '13

Hi Siddharth can you cc the list so others can answer? Did you check the norm to make sure it's ok? You can definitely take the mri_cc from 5.3 and use the rest of 5.1. If you let us know your hardware/software environment we'll send you an updated binary, but as I said it's usually a symptom of something else going wrong Bruce On Thu, 16 May 2013, Ray, Siddharth wrote: > Hi Bruce, > > Thanks for the prompt reply. I am using 5.1 version and I don’t think I can switch to a new version because I already have subjects processed using this one. > > So do we have any fix for this version? > > Please let me know. > > -Siddharth > > -----Original Message----- > From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] > Sent: Thursday, May 16, 2013 2:08 PM > To: Ray, Siddharth > Cc: freesurfer(a)nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] F Problem running : mri_cc -aseg.auto_ > > Hi Siddharth > > what FS version are you running? I did fix this recently, and the fix is certainly in 5.3. It only happened if there was something badly wrong, like the norm.mgz being empty for example, so it was more a symptom of an earlier failure then a problem of it's own (although I did have it print out an error message instead of running forever) > > > cheers > Bruce > > On Thu, 16 May 2013, Ray, > Siddharth wrote: > >> >> Hi, >> >> >> >> I am new to freesurfer and was trying to run it on couple of my >> subjects but I am stuck (for last 40 hrs) at stage >> >> >> >> “mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz -lta >> /home/sray2/Desktop/combirx/cr052_ip_output/mri/transforms/cc_up.lta >> cr052_ip_output” >> >> >> >> it seems. The last few lines of the log file were: >> >> >> >> searching scale 1 Z rot 9.9 >> >> searching scale 1 Z rot 10.1 global minimum found at slice 122.0, >> rotations (-3.99, 3.36) >> >> final transformation (x=122.0, yr=-3.992, zr=3.355): >> >> 0.996 -0.059 -0.069 25.704; >> >> 0.058 0.998 -0.004 -3.212; >> >> 0.070 0.000 0.998 -51.078; >> >> 0.000 0.000 0.000 1.000; >> >> >> >> >> >> Have anyone came across this error before ? and know how to fix this. >> Please let me know. >> >> >> >> Thanks in advance. >> >> >> >> ~Siddharth Ray >> >> >> >> P.S. I have attached the log file here. >> >> >> > > > 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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Re: [Freesurfer] Tracula problem
by Anastasia Yendiki 20 May '13

20 May '13

Hi Matt - Yes, the dcmroot variable can be used if you have the same root directory for *all* input files. If not, don't define dcmroot and instead give the full path to each input file. Then you shouldn't have to modify any scrips. a.y On Fri, 17 May 2013, Hoptman, Matthew wrote: > Hi Anastasia, > I solved this particular problem in a new dmrirc, but it seemed that I had to modify trac-all to remove the ${dcmroot} in front of: > infile, b0mfile and b0pfile: > > diff bin/trac-preproc bin/trac-preproc.orig > > < if ($#dcmroot > 0) set infile = $infile > --- >> if ($#dcmroot > 0) set infile = $dcmroot/$infile > 259c259 > < endif > --- >> endif > 296c296 > < set dcmfile = $b0mfile > --- >> set dcmfile = $dcmroot/$b0mfile > 311c311 > < set dcmfile = $b0pfile > --- >> set dcmfile = $dcmroot/$b0pfile > > But now it doesn't seem to loop through the subjects, so I'm doing them one at a time (painful). > > Also, if, as in my other question, I try to run this as a cluster job, I don't know how I can substitute a new subject into subjlist. I have 64 subjects and would like to do trac-all -prep -c dmri on all of them simultaneously. I have used bedpostx in SGE, but there you can just write loop to get it to go through your subjects. > > If I could make the subject variable external to dmrirc, I could do easily script the trac-all job to run in SGE, but I can't fiugre out how to pass it to the trac-all command. Is there any way to pass the subject number directly to the command? > Does this make sense? > Matt > > -----Original Message----- > From: Anastasia Yendiki [mailto:ayendiki@nmr.mgh.harvard.edu] > Sent: Friday, May 17, 2013 12:31 PM > To: Hoptman, Matthew > Cc: freesurfer(a)nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] Tracula problem > > > Hi Matt - Can you source try this on the command line: > source dmrirc_53beta > echo $b0mlist > echo $b0plist > > Are these filenames correct, do these files exist? This is how you define > them in your configuration file: > set b0mlist = (`ls ${subjlist}/fmag/MR.* | sort -n | head -1`) > set b0plist = (`ls ${SUBJECTS_DIR}/${subjlist}/fphas/ | sort -n | head -1`) > > Thanks, > a.y > > On Wed, 15 May 2013, Hoptman, Matthew wrote: > >> >> Hi all, >> >> >> >> I’m having a problem with tracula. I’m trying to run in version 5.3 beta (is that >> version very different from the newer 5.3?). If I run >> >> trac-preproc -c dmrirc –prep, >> >> >> I get: >> >> mri_convert /home/hoptman/freesurfer/subjects/c159032/ >> /home/hoptman/freesurfer/subjects/c159032/dmri/b0mag.nii.gz >> >> mri_convert /home/hoptman/freesurfer/subjects/c159032/ >> /home/hoptman/freesurfer/subjects/c159032/dmri/b0mag.nii.gz >> >> corRead(): can't open file /home/hoptman/freesurfer/subjects/c159032/COR-.info >> >> >> >> I don’t know why it would look for COR-.info in the subjects’ root directory. I’m >> attaching my dmrirc file in case that helps. >> >> >> >> Thanks, >> Matt >> >> Matthew J. Hoptman, PhD >> Research Scientist V >> Nathan S. Kline Institute for Psychiatric Research >> >> Research Associate Professor in Psychiatry >> NYU School of Medicine >> >> >> >> IMPORTANT NOTICE: This e-mail is meant only for the use of the intended recipient. >> It may contain confidential information which is legally privileged or otherwise >> protected by law. If you received this >> e-mail in error or from someone who was not authorized to send it to you, you are >> strictly prohibited from reviewing, using, disseminating, distributing or copying >> the e-mail. >> >> PLEASE NOTIFY US IMMEDIATELY OF THE ERROR BY RETURN E-MAIL AND DELETE THIS MESSAGE >> FROM YOUR SYSTEM. Thank you for your cooperation. >> >> >> >> __________________________________________________________________________________ >> Conserve Resources. Print only when necessary. >> >> IMPORTANT NOTICE: This e-mail is meant only for the use of the intended recipient. >> It may contain confidential information which is legally privilegedor otherwise >> protected by law. If you received this e-mail in error or from someone who is not >> authorized to send it to you, you are strictly prohibited from reviewing, using, >> disseminating, distributing or copying the e-mail. PLEASE NOTIFY US IMMEDIATELY OF >> THE ERROR BY RETURN E-MAIL AND DELETE THIS MESSAGE FROM YOUR SYSTEM. Thank you for >> your cooperation. >> >> IMPORTANT NOTICE: This e-mail is meant only for the use of the intended recipient. >> It may contain confidential information which is legally privileged or otherwise >> protected by law. If you received this e-mail in error or from someone who is not >> authorized to send it to you, you are strictly prohibited from reviewing, using, >> disseminating, distributing or copying the e-mail. PLEASE NOTIFY US IMMEDIATELY OF >> THE ERROR BY RETURN E-MAIL AND DELETE THIS MESSAGE FROM YOUR SYSTEM. Thank you for >> your cooperation. >> > > > 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. > > > Conserve Resources. Print only when necessary. > > IMPORTANT NOTICE: This e-mail is meant only for the use of the intended recipient. It may contain confidential information which is legally privilegedor otherwise protected by law. If you received this e-mail in error or from someone who is not authorized to send it to you, you are strictly prohibited from reviewing, using, disseminating, distributing or copying the e-mail. PLEASE NOTIFY US IMMEDIATELY OF THE ERROR BY RETURN E-MAIL AND DELETE THIS MESSAGE FROM YOUR SYSTEM. Thank you for your cooperation. > IMPORTANT NOTICE: This e-mail is meant only for the use of the intended recipient. It may contain confidential information which is legally privileged or otherwise protected by law. If you received this e-mail in error or from someone who is not authorized to send it to you, you are strictly prohibited from reviewing, using, disseminating, distributing or copying the e-mail. PLEASE NOTIFY US IMMEDIATELY OF THE ERROR BY RETURN E-MAIL AND DELETE THIS MESSAGE FROM YOUR SYSTEM. Thank you for your cooperation. >

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Tracula longitudinal "nan" values for highest probability path
by vbrunsch＠nmr.mgh.harvard.edu 20 May '13

20 May '13

Dear Anastasia, When running the longitudinal tracula version on our 39 subjects I found for some of them "nan"-values for the center_avg variables of some tracts. When I have a look at the tract distribution and the highest probability path, everything seems to be ok. However, when checking the control points of this path, two of them are the same. Do you know how this could have happened / what to do? E.g. control points of forceps major from a subject (cpts.map.txt), see 4th and 5th control point: 63 20 39 67 31 39 59 43 38 52 42 38 52 42 38 43 32 38 50 19 33 And the respective pathstats.overall.txt: Count 1500 Volume 370 Len_Min 62 Len_Max 99 Len_Avg 78.9307 Len_Center 0 AD_Avg 0.00155598 AD_Avg_Weight 0.00158424 AD_Avg_Center -nan RD_Avg 0.000438439 RD_Avg_Weight 0.000401328 RD_Avg_Center -nan MD_Avg 0.000810952 MD_Avg_Weight 0.000795633 MD_Avg_Center -nan FA_Avg 0.662419 FA_Avg_Weight 0.696257 FA_Avg_Center -nan Thanks for your help!! :) Best, Vincent

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DTI metrics along the whole tract?
by celine＠nmr.mgh.harvard.edu 20 May '13

20 May '13

Hi Tracula team I am using tracula to study the corticospinal tract in a patient population. I am wondering if there would be a way to have the different DTI metrics from the whole tract at different depth/portion of the tracts. Something like the information given by the pathstats.byvoxel.txt file, but for the whole width of the tract? If not, do you see a way to sample the value of the diffusion metrics on a certain tract starting from the cortex (like with projfrac or projdist with the WM surface)? Thanks very much for your help Celine -- Celine Louapre, MD Research Fellow at Massachusetts General Hospital Department of Radiology, MGH Building 149, Room 2301 13th Street Charlestown, MA 02129

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How to extract subjects' volume based on mask from spm?
by zhang mingxia 20 May '13

20 May '13

Dear Freesurfer experts, I analyzed functional data by spm and made a mask (analyze format). I have also run recon-all of structural data. My question is: how to extract mean volume (from structural data) of the mask(from spm)? I only extracted volume(or thickness) of ROI of a label edited by myself and annotation file. If I can convert analyze format to a label or annotation file, I can use that method. But how to convert analyze format to a label or annotation? Or is there any easy way? Thanks in advance! Mingxia Zhang

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Freesurfer May 2013