Freesurfer December 2015

freesurfer@nmr.mgh.harvard.edu

115 participants
187 discussions

Re: [Freesurfer] Freesurfer question
by Douglas N Greve 21 Dec '15

21 Dec '15

Sorry for the delay. Answers below On 12/21/2015 03:58 PM, Woo, Jonghye wrote: > Dear Doug, > > I have following questions: I posted the question but no one answered it. > > 1. What is the best way to convert annotation to the segmentation mask > (volume)? mri_label2vol. Specify the annotation with the --annot flag. Run with --help to get more help. > > 2. I also asked the questions below. > I tried to use PALS B12 mask in fsaverage, and try to create a volume > mask (from the annot file). I used the command below: > mri_aparc2aseg --s my_subject --annot PALS_B12_Brodmann --o > PALS_B12_Brodmann_Mask.nii --annot-table lh_PALS_B12_table.txt > I’ve got the table from this command: mis_info > lh.PALS_B12_Brodmann.annot & mis_info rh.PALS_B12_Brodmann.annot > (https://surfer.nmr.mgh.harvard.edu/fswiki/PALS_B12) > After creating the mask, I compared the table and the mask but they > are not corresponding. Rather the labels in the segmentation mask was > corresponding to FreeSurferColorLUT.txt. How are you viewing this? If in tkmedit or freeview, are you specifying a color table? > > Do you have any suggestions? Thank you in advance. > > Best, > Jonghye > >> On Dec 21, 2015, at 11:50 AM, Douglas N Greve >> <greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote: >> >> Hi Jonghye, is this something that can be handled over email? Is is >> something that cannot be posted to the list? >> doug >> >> >> On 12/16/2015 11:08 AM, Woo, Jonghye wrote: >>> >>> Dear Doug, >>> >>> My name is Jonghye and I have a quick question in freesurfer. Can I >>> drop by your office for get some information this afternoon? Looking >>> forward to hearing from you. >>> >>> Best, >>> Jonghye >>> >>> >> >> -- >> Douglas N. Greve, Ph.D. >> MGH-NMR Center >> greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> >> Phone Number: 617-724-2358 >> Fax: 617-726-7422 >> >> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 >> www.nmr.mgh.harvard.edu/facility/filedrop/index.html >> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ >> > -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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R: Re: R: Re: R: R: Re: R: Re: FDR in FS-FAST
by stdp82＠virgilio.it 21 Dec '15

21 Dec '15

yes and this is the error: mri_fdr dyld: Library not loaded: @executable_path/../lib/gcc/lib/libstdc++.6. dylib Referenced from: /Applications/freesurfer/bin/mri_fdr Reason: image not found Trace/BPT trap >----Messaggio originale---- >Da: greve(a)nmr.mgh.harvard.edu >Data: 21-dic-2015 20.04 >A: <freesurfer(a)nmr.mgh.harvard.edu> >Ogg: Re: [Freesurfer] R: Re: R: R: Re: R: Re: FDR in FS-FAST > >have you tried changing the permission to be exectuable? >chmod a+x mri_fdr > >On 12/21/2015 02:02 PM, stdp82(a)virgilio.it wrote: >> Thanks but permission denied persist. >> >> >>> ----Messaggio originale---- >>> Da: greve(a)nmr.mgh.harvard.edu >>> Data: 21-dic-2015 17.33 >>> A: <freesurfer(a)nmr.mgh.harvard.edu> >>> Ogg: Re: [Freesurfer] R: R: Re: R: Re: FDR in FS-FAST >>> >>> >>> Try this version for mac >>> ftp://surfer.nmr.mgh.harvard. edu/transfer/outgoing/flat/greve/mri_fdr. >> osx >>> Use mri_surfcluster (or mri_volcluster) to do the clustering >>> >>> >>> On 12/18/2015 05:11 PM, stdp82(a)virgilio.it wrote: >>>> I have run >>>> mri_fdr --help >>>> but I obtained this warning: >>>> /Applications/freesurfer/bin/mri_fdr: Permission denied. >>>> >>>> I would also ask you if is possible to threshold the FDR map (p<0. >>>> 05), >>>> eliminating clusters < 5 voxels. >>>> >>>> Thanks >>>> >>>> >>>> Stefano >>>> >>>> >>>> >>>>>> ----Messaggio originale---- >>>>>> Da: greve(a)nmr.mgh.harvard.edu >>>>>> Data: 11-dic-2015 20.23 >>>>>> A: <freesurfer(a)nmr.mgh.harvard.edu> >>>>>> Ogg: Re: [Freesurfer] R: Re: FDR in FS-FAST >>>>>> >>>>>> $FREESURFER_HOME/bin >>>>>> >>>>>> On 12/11/15 2:08 PM, stdp82(a)virgilio.it wrote: >>>>>>> Thanks, in which folder I should put this file? >>>>>>> >>>>>>> Stefano >>>>>>> >>>>>>> >>>>>>>> ----Messaggio originale---- >>>>>>>> Da: greve(a)nmr.mgh.harvard.edu >>>>>>>> Data: 7-dic-2015 19.23 >>>>>>>> A: <freesurfer(a)nmr.mgh.harvard.edu> >>>>>>>> Ogg: Re: [Freesurfer] FDR in FS-FAST >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> On 12/07/2015 08:35 AM, stdp82(a)virgilio.it wrote: >>>>>>>>> Hi list, >>>>>>>>> I have two concerns, please: >>>>>>>>> 1) It is possible to apply FDR correction on rs-fMRI seed >> based >>>>>>>>> analysis by FS-FAST? If yes, I can I do it? >>>>>>>> try this binary >>>>>>>> ftp://surfer.nmr.mgh.harvard. >>>>> edu/transfer/outgoing/flat/greve/mri_fdr >>>>>>>>> 2) I have apply the FS guidelines and I have used Montecarlo >>>>>>>>> correction with threshold at 1.3 but in the within group >>>> analysis >>>>>>> the >>>>>>>>> clusters are very large. In the guide I read examples with a >>>>>>> threshold >>>>>>>>> at 3. Is there a specific reason? >>>>>>>> There is not a hard-and-fast criteria for the voxel-wise >>>>> threshold. 3 >>>>>>> is >>>>>>>> fine as is 1.3 >>>>>>>>> Thanks >>>>>>>>> >>>>>>>>> Stefano >>>>>>>>> >>>>>>>>> >>>>>>>>> _______________________________________________ >>>>>>>>> Freesurfer mailing list >>>>>>>>> Freesurfer(a)nmr.mgh.harvard.edu >>>>>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>>>>> -- >>>>>>>> Douglas N. Greve, Ph.D. >>>>>>>> MGH-NMR Center >>>>>>>> greve(a)nmr.mgh.harvard.edu >>>>>>>> Phone Number: 617-724-2358 >>>>>>>> Fax: 617-726-7422 >>>>>>>> >>>>>>>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >>>>>>>> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 >>>>>>>> www.nmr.mgh.harvard.edu/facility/filedrop/index.html >>>>>>>> Outgoing: ftp://surfer.nmr.mgh.harvard. >>>>>>> edu/transfer/outgoing/flat/greve/ >>>>>>>> _______________________________________________ >>>>>>>> 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. >>>>>>>> >>>>>>>> >>>>>>> _______________________________________________ >>>>>>> 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 >>>>>> >>>>> _______________________________________________ >>>>> 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 >>>> >>>> >>> -- >>> Douglas N. Greve, Ph.D. >>> MGH-NMR Center >>> greve(a)nmr.mgh.harvard.edu >>> Phone Number: 617-724-2358 >>> Fax: 617-726-7422 >>> >>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >>> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 >>> www.nmr.mgh.harvard.edu/facility/filedrop/index.html >>> Outgoing: ftp://surfer.nmr.mgh.harvard. >> edu/transfer/outgoing/flat/greve/ >>> _______________________________________________ >>> 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 >> >> > >-- >Douglas N. Greve, Ph.D. >MGH-NMR Center >greve(a)nmr.mgh.harvard.edu >Phone Number: 617-724-2358 >Fax: 617-726-7422 > >Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 >www.nmr.mgh.harvard.edu/facility/filedrop/index.html >Outgoing: ftp://surfer.nmr.mgh.harvard. edu/transfer/outgoing/flat/greve/ > >_______________________________________________ >Freesurfer mailing list >Freesurfer(a)nmr.mgh.harvard.edu >https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >

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R: Re: R: R: Re: R: Re: FDR in FS-FAST
by stdp82＠virgilio.it 21 Dec '15

21 Dec '15

Thanks but permission denied persist. >----Messaggio originale---- >Da: greve(a)nmr.mgh.harvard.edu >Data: 21-dic-2015 17.33 >A: <freesurfer(a)nmr.mgh.harvard.edu> >Ogg: Re: [Freesurfer] R: R: Re: R: Re: FDR in FS-FAST > > >Try this version for mac >ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_fdr. osx > >Use mri_surfcluster (or mri_volcluster) to do the clustering > > >On 12/18/2015 05:11 PM, stdp82(a)virgilio.it wrote: >> I have run >> mri_fdr --help >> but I obtained this warning: >> /Applications/freesurfer/bin/mri_fdr: Permission denied. >> >> I would also ask you if is possible to threshold the FDR map (p<0. >> 05), >> eliminating clusters < 5 voxels. >> >> Thanks >> >> >> Stefano >> >> >> >>>> ----Messaggio originale---- >>>> Da: greve(a)nmr.mgh.harvard.edu >>>> Data: 11-dic-2015 20.23 >>>> A: <freesurfer(a)nmr.mgh.harvard.edu> >>>> Ogg: Re: [Freesurfer] R: Re: FDR in FS-FAST >>>> >>>> $FREESURFER_HOME/bin >>>> >>>> On 12/11/15 2:08 PM, stdp82(a)virgilio.it wrote: >>>>> Thanks, in which folder I should put this file? >>>>> >>>>> Stefano >>>>> >>>>> >>>>>> ----Messaggio originale---- >>>>>> Da: greve(a)nmr.mgh.harvard.edu >>>>>> Data: 7-dic-2015 19.23 >>>>>> A: <freesurfer(a)nmr.mgh.harvard.edu> >>>>>> Ogg: Re: [Freesurfer] FDR in FS-FAST >>>>>> >>>>>> >>>>>> >>>>>> On 12/07/2015 08:35 AM, stdp82(a)virgilio.it wrote: >>>>>>> Hi list, >>>>>>> I have two concerns, please: >>>>>>> 1) It is possible to apply FDR correction on rs-fMRI seed based >>>>>>> analysis by FS-FAST? If yes, I can I do it? >>>>>> try this binary >>>>>> ftp://surfer.nmr.mgh.harvard. >>> edu/transfer/outgoing/flat/greve/mri_fdr >>>>>>> 2) I have apply the FS guidelines and I have used Montecarlo >>>>>>> correction with threshold at 1.3 but in the within group >> analysis >>>>> the >>>>>>> clusters are very large. In the guide I read examples with a >>>>> threshold >>>>>>> at 3. Is there a specific reason? >>>>>> There is not a hard-and-fast criteria for the voxel-wise >>> threshold. 3 >>>>> is >>>>>> fine as is 1.3 >>>>>>> Thanks >>>>>>> >>>>>>> Stefano >>>>>>> >>>>>>> >>>>>>> _______________________________________________ >>>>>>> Freesurfer mailing list >>>>>>> Freesurfer(a)nmr.mgh.harvard.edu >>>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>>> -- >>>>>> Douglas N. Greve, Ph.D. >>>>>> MGH-NMR Center >>>>>> greve(a)nmr.mgh.harvard.edu >>>>>> Phone Number: 617-724-2358 >>>>>> Fax: 617-726-7422 >>>>>> >>>>>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >>>>>> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 >>>>>> www.nmr.mgh.harvard.edu/facility/filedrop/index.html >>>>>> Outgoing: ftp://surfer.nmr.mgh.harvard. >>>>> edu/transfer/outgoing/flat/greve/ >>>>>> _______________________________________________ >>>>>> 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. >>>>>> >>>>>> >>>>> _______________________________________________ >>>>> 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 >>>> >>> _______________________________________________ >>> 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 >> >> > >-- >Douglas N. Greve, Ph.D. >MGH-NMR Center >greve(a)nmr.mgh.harvard.edu >Phone Number: 617-724-2358 >Fax: 617-726-7422 > >Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 >www.nmr.mgh.harvard.edu/facility/filedrop/index.html >Outgoing: ftp://surfer.nmr.mgh.harvard. edu/transfer/outgoing/flat/greve/ > >_______________________________________________ >Freesurfer mailing list >Freesurfer(a)nmr.mgh.harvard.edu >https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >

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Hippocampal Subfields on 1.5 Tesla - Freesufer v. 6
by Douglas Merkitch 21 Dec '15

21 Dec '15

Hello Freesurfer experts, I am wondering if the new hippocampal subfields (HSF) module that will be included in Freesurfer v. 6 would work with 1.5 Tesla data. Upon reviewing the mail archives, I came across a thread (https://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg35665.html) regarding the validity of using 1.5 Tesla T1 data with the older HSF module from Freesurfer v. 5.3. My takeaway from this thread is that the older module should work reasonably well as long as the T1 data is 1mm, regardless of whether the data is 1.5 or 3 Tesla (but please correct me if I am wrong!). Would the same apply for the new HSF module in Freesurfer v. 6 when it is officially released? Any insight would be greatly appreciated! Thanks, Doug Douglas Merkitch Neurological Sciences Rush University Medical Center Email: Douglas_Merkitch(a)rush.edu<mailto:Douglas_Merkitch@rush.edu>

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Pial Surface, total area?
by Guido Orlando Pascariello 21 Dec '15

21 Dec '15

Hi FS Experts I want to get the total area from pia cortex, in order to normalize the parcellations measure. In lh.aparc.statsfile on there is a line: # Measure Cortex, WhiteSurfArea, White Surface Total Area, ****** mm^2 > I've looking for this topic in the lista and I found there is a way to get PialSurfArea. However I wonder if needed to achieve my goal. I mean, why doesn't recon-all measure this area? Is WhiteSurfArea enought to normalice the parcellations? I'll be grateful if you can help Being all for now, I await a reply Guido PASCARIELLO Facultad de Ingeniería - Universidad Nacional de Entre Ríos Argentina

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no aseg.stats after recon-all -all?
by Schweren, LJS (med) 21 Dec '15

21 Dec '15

Dear Freesurfer experts, I'm trying to get BrainSeg for 5 subjects. I'm running the following commands: for scan in ... do cd $SUBJECTS_DIR recon-all -all -subjid $scan done It completes recon-all, but with errors. These are the errors: [me@mycomp]$ cat recon-all.error ------------------------------ SUBJECT [mysubj] DATE Thu Dec 17 12:57:00 PST 2015 USER me HOST mycomp PROCESSOR x86_64 OS Linux Linux emotion.ucsd.edu 2.6.18-406.el5 #1 SMP Tue Jun 2 17:25:57 EDT 2015 x86_64 x86_64 x86_64 GNU/Linux $Id: recon-all,v 1.379.2.73 2013/05/12 23:15:37 nicks Exp $ /usr/local/freesurfer/bin/recon-all PWD /[mypathtoSUBJECTS_DIR]/[mysubj]/scripts CMD mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 [mysubj] lh ../surf/lh.sphere.reg /usr/local/freesurfer5/average/lh.DKTatlas40.gcs ../label/lh.aparc.DKTatlas40.annot [me@mycomp]$ cat error.log GCSAread(/usr/local/freesurfer5/average/lh.DKTatlas40.gcs): could not open file As a result, I don't have any aseg.stats, nor any aparc+aseg files. I ran mri_segstats separately, but then I only get the subcortical volumes, not the totals. If I include the --brain-vol-from-seg flag, it errors again, saying: $Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $ cwd cmdline mri_segstats --seg /[mypathtoSUBJECTS_DIR]/[mysubj]/mri/aseg.mgz --brain-vol-from-seg --ctab /usr/local/freesurfer5/FreeSurferColorLUT.txt --excludeid 0 --sum /[mypathtoSUBJECTS_DIR]/scripts/[mysubj].aseg.sum sysname Linux hostname mycomp machine x86_64 user me UseRobust 0 Loading /[mypathtoSUBJECTS_DIR]/[mysubj]/mri/aseg.mgz Getting Brain Volume Statistics MRISread(/[mypathtoSUBJECTS_DIR]/(null)/surf/lh.white): could not open file No such file or directory I'm hoping you can help me! My goal is to get just BrainSeg for these subjects, I don't need the other outcomes. So if there is a work-around I would be happy to hear. Thank you for your help! All my best, Lizanne ________________________________ De inhoud van dit bericht is vertrouwelijk en alleen bestemd voor de geadresseerde(n). Anderen dan de geadresseerde(n) mogen geen gebruik maken van dit bericht, het niet openbaar maken of op enige wijze verspreiden of vermenigvuldigen. Het UMCG kan niet aansprakelijk gesteld worden voor een incomplete aankomst of vertraging van dit verzonden bericht. The contents of this message are confidential and only intended for the eyes of the addressee(s). Others than the addressee(s) are not allowed to use this message, to make it public or to distribute or multiply this message in any way. The UMCG cannot be held responsible for incomplete reception or delay of this transferred message.

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R: R: Re: R: Re: FDR in FS-FAST
by stdp82＠virgilio.it 21 Dec '15

21 Dec '15

I have run mri_fdr --help but I obtained this warning: /Applications/freesurfer/bin/mri_fdr: Permission denied. I would also ask you if is possible to threshold the FDR map (p<0. 05), eliminating clusters < 5 voxels. Thanks Stefano >>----Messaggio originale---- >>Da: greve(a)nmr.mgh.harvard.edu >>Data: 11-dic-2015 20.23 >>A: <freesurfer(a)nmr.mgh.harvard.edu> >>Ogg: Re: [Freesurfer] R: Re: FDR in FS-FAST >> >>$FREESURFER_HOME/bin >> >>On 12/11/15 2:08 PM, stdp82(a)virgilio.it wrote: >>> Thanks, in which folder I should put this file? >>> >>> Stefano >>> >>> >>>> ----Messaggio originale---- >>>> Da: greve(a)nmr.mgh.harvard.edu >>>> Data: 7-dic-2015 19.23 >>>> A: <freesurfer(a)nmr.mgh.harvard.edu> >>>> Ogg: Re: [Freesurfer] FDR in FS-FAST >>>> >>>> >>>> >>>> On 12/07/2015 08:35 AM, stdp82(a)virgilio.it wrote: >>>>> Hi list, >>>>> I have two concerns, please: >>>>> 1) It is possible to apply FDR correction on rs-fMRI seed based >>>>> analysis by FS-FAST? If yes, I can I do it? >>>> try this binary >>>> ftp://surfer.nmr.mgh.harvard. >edu/transfer/outgoing/flat/greve/mri_fdr >>>>> 2) I have apply the FS guidelines and I have used Montecarlo >>>>> correction with threshold at 1.3 but in the within group analysis >>> the >>>>> clusters are very large. In the guide I read examples with a >>> threshold >>>>> at 3. Is there a specific reason? >>>> There is not a hard-and-fast criteria for the voxel-wise >threshold. 3 >>> is >>>> fine as is 1.3 >>>>> Thanks >>>>> >>>>> Stefano >>>>> >>>>> >>>>> _______________________________________________ >>>>> Freesurfer mailing list >>>>> Freesurfer(a)nmr.mgh.harvard.edu >>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>> -- >>>> Douglas N. Greve, Ph.D. >>>> MGH-NMR Center >>>> greve(a)nmr.mgh.harvard.edu >>>> Phone Number: 617-724-2358 >>>> Fax: 617-726-7422 >>>> >>>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >>>> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 >>>> www.nmr.mgh.harvard.edu/facility/filedrop/index.html >>>> Outgoing: ftp://surfer.nmr.mgh.harvard. >>> edu/transfer/outgoing/flat/greve/ >>>> _______________________________________________ >>>> 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. >>>> >>>> >>> _______________________________________________ >>> 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 >> > >_______________________________________________ >Freesurfer mailing list >Freesurfer(a)nmr.mgh.harvard.edu >https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >

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Z-score from .label
by stdp82＠virgilio.it 21 Dec '15

21 Dec '15

Hi list, I would like to extract the mean z-score from a roi.label in each subject after FS-FAST (rs-fMRI seed based).How can I do? Thanks Stefano

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segmentation fault (core dumped)
by Fengji Geng 21 Dec '15

21 Dec '15

Dear freesurfer developers and users, I encountered an error as 'segmentation fault (core dumped)' when I run 'recon-all -all -s $s -hippocampal-subfields-T1T2 $s/T2/*.mgz T1T2'. Attached is the error log. The version of freesurfer is 'freesurfer-Linux-centos6_x86_64-dev-20151006'. Here goes our server information: LSB Version: :base-4.0-amd64:base-4.0-ia32:base-4.0-noarch:core-4.0-amd64:core-4.0-ia32:core-4.0-noarch:graphics-4.0-amd64:graphics-4.0-ia32:graphics-4.0-noarch:printing-4.0-amd64:printing-4.0-ia32:printing-4.0-noarch Distributor ID: RedHatEnterpriseServer Description: Red Hat Enterprise Linux Server release 6.6 (Santiago) Release: 6.6 Thank you in advance for your help. ----- Fengji

2 2

Qdec
by Caroline Beelen 21 Dec '15

21 Dec '15

Dear Freesurfer experts, I just started using Freesurfer for performing MRI (T1)- group-based ROI analysis and managed to go through the first recon-all processing stream and making few manual edits. Then I followed first steps of the Qdec -procedure. However, there is a separate section on ROI-analysis as well. Are they complementary or not (which one to follow best)? I tried both. However, at the Qdec section I got lost at creating the table: how to know volumes of pre-specified structures? At the ROI-section I got lost at the point of adding labels to the average subject: cd $freesurfer (directory) mri_label2label \ --srcsubject avgsubject \ --srclabel avgsubject/label/lh.BA45.label \ --trgsubject A06_T1 \ --trglabel A06_T1/label/lh.BA45.label \ --hemi lh \ --regmethod surface (followed the example) I got the error of: subject_dir .../freesurfer Freesurfer_home .../freesurfer Loading source lab: 'no such file or directory'...etc. ... ERROR reading lh.BA45.label. What am I doing wrong? Thank you very much for your response in advance. Kind regards, Caroline

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2005

2004

Freesurfer December 2015