Freesurfer

freesurfer@nmr.mgh.harvard.edu

16 participants
30084 discussions

variable TR
by shahin＠nmr.mgh.harvard.edu 22 Dec '15

22 Dec '15

Hi Surfers We are wondering if we can use freesurfer to analyze ECG-gated fmri. As far as I see, mkanalysis-sess expects a fix TR. Since we are in the design stage, any hint or suggestion to facilitate future data analysis will be highly appreciated. Regards

2 1

Re: [Freesurfer] Help importing files from a previous SPM analysis
by Luis Fernado Silva Castro de Araújo 21 Dec '15

21 Dec '15

Dear Douglas, It's an anatomical analysis. Perhaps I misunderstood the requirement for setting up the directories in the FSFAST for the recon-all command. If that is the case, it is then a matter of converting my img files into mgz and run recon-all on them, am I right? Does the command recon-all also gives me volumes for specific Brodmann's areas? Or do I have to run a labeling to that? Thank you, luis

3 4

Error in QDEC -"Generate Stats Data Tables"
by nellie 21 Dec '15

21 Dec '15

Hi Freesurfer experts,When I tried to use "Generate Stats Data Tables" in QDEC, some errors came out. The related screenshot is attached in this letter, and I found there wasn't any folder named "pubsw" in the "usr". I wonder how to fix these errors? Thanks a lot. Best, Amolie

2 1

qdec
by levi solomyak 21 Dec '15

21 Dec '15

Dear experts, I've been attempting to generate a stats data table in qdec, but each time I get a "Index Error: list index is out of range" error. This is occurring when it is trying to parse the .stats file. I've made sure that the files all line up exactly with the qdec table and that SUBJECTS_DIR is properly sourced so I'm not sure how to fix this problem. Any help would be greatly appreciated! Here are the details of the errors: 1) machine being used: Linux localhost.localdomain 3.10.0-229.4.2.el7.x86_64 #1 SMP Wed May 13 10:06:09 UTC 2015 x86_64 x86_64 x86_64 GNU/Linux 2) Freesurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0-HCP 3) Current working directory: /projects/IndivRITL/data/leviDiff/Subjects 4) which qdec : /usr/local/freesurfer/bin/qdec 5) After loading the gui, I attempted to generate a qdec stats table. This is the error that was returned: ----------------------------------------------------------------------------------- asegstats2table --common-segs --meas volume --tablefile /mnt/engram/projects/IndivRITL/data/leviDiff/Subjects/qdec/stats_tables/aseg.volume.stats.dat --statsfile=aseg.stats --subjects 100307 101006 104820 105115 110411 111312 111413 111716 112819 113215 113619 113922 114419 115320 116524 117122 117324 118528 135225 135932 150625 150726 151223 151526 170934 171633 172130 172332 172534 172938 173334 175439 177645 177746 178142 200109 200614 201111 201414 201818 203418 204016 204521 304020 307127 308331 310621 316633 329440 365343 366042 377451 380036 385450 386250 412528 433839 436239 480141 486759 497865 499566 500222 510326 530635 531536 540436 561242 562446 565452 566454 567052 567961 568963 571548 580044 580347 581349 583858 586460 594156 598568 599671 SUBJECTS_DIR : /mnt/engram/projects/IndivRITL/data/leviDiff/Subjects Parsing the .stats files Traceback (most recent call last): File "/usr/local/freesurfer/bin/asegstats2table", line 538, in <module> id_name_map, measurelist = parsed.parse(options.meas) File "/home/usr/local/freesurfer/bin/fsutils.py", line 115, in parse self.id_name_map[seg] = strlst[4] # Col 4 is Seg Name IndexError: list index out of range ERROR: In /usr/pubsw/packages/KWWidgets/CVS-vtk560/KWWidgets/vtkKWTkUtilities.cxx, line 230 vtkKWQdecApp (0x278d8060): Script: vtkTemp2 GenerateStatsDataTables Returned Error on line 1: Uncaught exception: command failed: asegstats2table --common-segs --meas volume --tablefile /mnt/engram/projects/IndivRITL/data/leviDiff/Subjects/qdec/stats_tables/aseg.volume.stats.dat --statsfile=aseg.stats --subjects 100307 101006 104820 105115 110411 111312 111413 111716 112819 113215 113619 113922 114419 115320 116524 117122 117324 118528 135225 135932 150625 150726 151223 151526 170934 171633 172130 172332 172534 172938 173334 175439 177645 177746 178142 200109 200614 201111 201414 201818 203418 204016 204521 304020 307127 308331 310621 316633 329440 365343 366042 377451 380036 385450 386250 412528 433839 436239 480141 486759 497865 499566 500222 510326 530635 531536 540436 561242 562446 565452 566454 567052 567961 568963 571548 580044 580347 581349 583858 586460 594156 598568 599671 Stack trace: Uncaught exception: command failed: asegstats2table --common-segs --meas volume --tablefile /mnt/engram/projects/IndivRITL/data/leviDiff/Subjects/qdec/stats_tables/aseg.volume.stats.dat --statsfile=aseg.stats --subjects 100307 101006 104820 105115 110411 111312 111413 111716 112819 113215 113619 113922 114419 115320 116524 117122 117324 118528 135225 135932 150625 150726 151223 151526 170934 171633 172130 172332 172534 172938 173334 175439 177645 177746 178142 200109 200614 201111 201414 201818 203418 204016 204521 304020 307127 308331 310621 316633 329440 365343 366042 377451 380036 385450 386250 412528 433839 436239 480141 486759 497865 499566 500222 510326 530635 531536 540436 561242 562446 565452 566454 567052 567961 568963 571548 580044 580347 581349 583858 586460 594156 598568 599671 while executing "vtkTemp2 GenerateStatsDataTables" ------------------------------------------------------------------------------------------------------- Thanks, LS -- Levi Solomyak Cole Neuroscience Laboratory (*colelab.org <http://colelab.org/>*) Center for Molecular and Behavioral Neuroscience (CMBN) Rutgers-Newark University

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

21 Dec '15

Hi Bruce, I have uploaded all the data to the server. The command that I run is 'recon-all -all -s $s -hippocampal-subfields-T1T2 $s/T2/*.mgz T1T2'. It would be great if you could keep us updated on how the fixing is going. Thanks! --------------------------------------------------------------------------------------------------------------------------------------- Message: 1 Date: Mon, 21 Dec 2015 10:38:08 -0500 (EST) From: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] FW: segmentation fault (core dumped) To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Message-ID: <alpine.LRH.2.20.1512211037340.22599(a)gate.nmr.mgh.harvard.edu> Content-Type: text/plain; charset="iso-8859-1" Hi Fengji hmmm, I don't remember ever seeing a core dump in mri-segstats before. If you upload the entire subject dir (tarred and gzipped) to our ftp site we will fix it. cheers Bruce ----- Fengji

2 1

Qdec visualization
by John Anderson 21 Dec '15

21 Dec '15

2 7

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 >

2 1

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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