Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30084 discussions

To normalize fMRI data in MNI152 template
by Kim, Gwang-Won 02 May '20

02 May '20

Dear expert, I’ like to normalize fMRI data in MNI152 template. Is it right?: “preproc-sess -s sess01 -fsd bold -stc up -surface fsaverage lhrh -cvs -fwhm 5 -per-run” Thanks, Gwang-Won

2 1

mri_glmfit
by jiahui 02 May '20

02 May '20

External Email - Use Caution Hello FreeSurfer Developers, I'm attempting to compare two groups' cortex, but for some of my subjects I get the following error when I run mri_glmfit \ --y rh.thickness.10.mgz \ --fsgd g3v1.fsgd dods\ --C group.mtx \ --surf fsaverage rh \ --cortex \ --glmdir g3v1.rh ERROR: DOF=0(this is error?) g3v1h.rh only 4 files(should have beta.mgh sig.mgz files...) I've searched the list and no similar errors have been reported. 1) FreeSurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c 2) Platform: ubuntu 16.04.6 LTS 3) mri_glmfit.log and figure01 figure02 figure03: see attached

1 0

Intensity inhomogeneity messing with the wm.mgz
by Zeng, Victor (BIDMC - Keshavan - Psychiatry) 02 May '20

02 May '20

Hi Freesurfer developers, I have a subsample of a FS dataset that have scanner-originated hyperintensities in the bilateral supramarginal/temporal lobes. I've manually removed these hyperintensities by editing the wm.mgz, yet FS seems to be unable to recognize these edits when looking at the ?h.white and aparc+aseg.mgz. Is there a possible way to rectify these errors? I am using FS6 for linux Here are some pictures: [cid:b4c23099-ffe0-4054-83b9-730a124b78e9]?[cid:35eb0541-c4de-4d31-9f85-4986e1e26661] Victor Zeng Beth Israel Deaconess Medical Center Keshavan Lab -- ________________________________ This message is intended for the use of the person(s) to whom it may be addressed. It may contain information that is privileged, confidential, or otherwise protected from disclosure under applicable law. If you are not the intended recipient, any dissemination, distribution, copying, or use of this information is prohibited. If you have received this message in error, please permanently delete it and immediately notify the sender. Thank you.

2 6

mri_glimfit error - help!
by Lab of Autism and Developmental Neuroscience, Lab of Autism and Developmental Neuroscience 01 May '20

01 May '20

External Email - Use Caution Dear Freesurfer experts, I'm having a persistent error with mri_glimfit. The fsgd file isn't being read correctly, despite following the exact requirements of the wiki. Also, the output mentions this "carriage returns warning", and despite running this conversion: cat fsgd_file.fsgd | sed 's/\r/\n/g' > new.fsgd_file.fsgd, the *new fsgd still doesn't work* (this code somehow alters the Group Descriptor at the top of the file, giving another error). I've attached my fsgd file (that I used while running the code below) Also, please see the full error of the glim_fit below: WARNING: carriage returns have been detected in file fsgd_file.fsgd Was it created on a Windows computer? This may cause an error in reading the FSGD file. If so, try running: cat fsgd_file.fsgd | sed 's/\r/\n/g' > new.fsgd_file.fsgd Then use new.fsgd_file.fsgd INFO: ignoring tag Tile INFO: ignoring tag nput INFO: ignoring tag nput INFO: gd2mtx_method is dods Reading source surface /Applications/freesurfer/BAP/group_analysis_data/qdec/fsaverage/surf/rh.white Number of vertices 163842 Number of faces 327680 Total area 65020.839844 AvgVtxArea 0.396851 AvgVtxDist 0.717994 StdVtxDist 0.193566 $Id: mri_glmfit.c,v 1.241.2.4 2016/12/08 22:02:40 zkaufman Exp $ cwd /Applications/freesurfer/BAP/group_analysis_data/qdec cmdline mri_glmfit.bin --y fsgd_RH_thickness.mgh --fsgd fsgd_file.fsgd dods --C contrasts.mtx --surf fsaverage rh --glmdir rhBAP_thickness.glmdir sysname Darwin hostname CCASPH-A1900447.cloud.ccas.gwu.edu machine x86_64 user ajobsaid FixVertexAreaFlag = 1 UseMaskWithSmoothing 1 OneSampleGroupMean 0 y /Applications/freesurfer/BAP/group_analysis_data/qdec/fsgd_RH_thickness.mgh logyflag 0 usedti 0 FSGD fsgd_file.fsgd labelmask /Applications/freesurfer/BAP/group_analysis_data/qdec/fsaverage/label/rh.cortex.label maskinv 0 glmdir rhBAP_thickness.glmdir IllCondOK 0 ReScaleX 1 DoFFx 0 Creating output directory rhBAP_thickness.glmdir Loading y from /Applications/freesurfer/BAP/group_analysis_data/qdec/fsgd_RH_thickness.mgh ... done reading. INFO: gd2mtx_method is dods Saving design matrix to rhBAP_thickness.glmdir/Xg.dat Computing normalized matrix Normalized matrix condition is 1e+10 Design matrix ------------------ -------------------------------- ERROR: matrix is ill-conditioned or badly scaled, condno = 1e+10 -------------------------------- Possible problem with experimental design: Check for duplicate entries and/or lack of range of continuous variables within a class. If you seek help with this problem, make sure to send: 1. Your command line: mri_glmfit.bin --y fsgd_RH_thickness.mgh --fsgd fsgd_file.fsgd dods --C contrasts.mtx --surf fsaverage rh --glmdir rhBAP_thickness.glmdir 2. The FSGD file (if using one) 3. And the design matrix above Attempting to diagnose further SumSq: Min=99999997952.000000 (col 0), Max=0.000000 (col 0) ... could not determine the cause of the problem Thanks! Alex Job

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Re: [Freesurfer] Which autorecon uses -hippocampal-subfields flags?
by Billah, Tashrif 01 May '20

01 May '20

Assuming `recon-all autorecon2 ...` requires completion of `recon-all autorecon1 ...` and autorecon3 requires completion of both 1 and 2, yes, I am asking which autorecon is sufficient. -Tashrif Are you asking whether you have to run recon-all all the way through in order to run the subfields or whether one of the autorecons is sufficient? On 5/1/2020 10:21 AM, Billah, Tashrif wrote: [Freesurfer] Which autorecon uses -hippocampal-subfields flags? <https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg65836.html> 2020-04-17 <https://www.mail-archive.com/search?l=freesurfer%40nmr.mgh.harvard.edu&q=da…>Thread <https://www.mail-archive.com/search?l=freesurfer%40nmr.mgh.harvard.edu&q=su…>Billah, Tashrif <https://www.mail-archive.com/search?l=freesurfer%40nmr.mgh.harvard.edu&q=fr…> Douglas, Let's try with an example. See the two waysT2 image can be integrated with recon-all Altogether: recon-all -subject subjectname -i /path/to/input_volume -T2 /path/to/T2_volume -T2pial -all autorecon3 only: recon-all -subject subjectname -T2 /path/to/T2_volume -T2pial -autorecon3 Similar to the former, -hippocampal-subfields-T1integrated with recon-all: recon-all -all -s bert -hippocampal-subfields-T1 Now the question, compared to the latter, which autorecon[1/2/3] would accept -hippocampal-subfields-T1? Does it make sense now? -Tashrif . ___ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer Re: [Freesurfer] Which autorecon uses -hippocampal-subfields flags? <https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg65832.html> 2020-04-17 <https://www.mail-archive.com/search?l=freesurfer%40nmr.mgh.harvard.edu&q=da…>Thread <https://www.mail-archive.com/search?l=freesurfer%40nmr.mgh.harvard.edu&q=su…>Douglas N. Greve <https://www.mail-archive.com/search?l=freesurfer%40nmr.mgh.harvard.edu&q=fr…> I don't understand the question. To run recon-all through to the end implies that you have run all the -autorecons On 4/17/2020 2:53 PM, Billah, Tashrif wrote: Right, I understand the rule about the scripts. However, my original question was about the subfields -hippocampal-subfields-T1/T2/T1T2 Again, can they be run with any of the autorecons separately? The example shown here <https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfields> integrates the subfileds with recon-all only but do no show combination with any autorecon commands. -Tashrif . *From:* Billah, Tashrif *Sent:* Friday, April 17, 2020 1:52 PM *To:* freesurfer(a)nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] Which autorecon uses -hippocampal-subfields flags? Douglas, A little more elaboration would help. What is "it" and what are "them"? -Tashrif . ___ 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 Re: [Freesurfer] Which autorecon uses -hippocampal-subfields flags? <https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg65829.html> 2020-04-17 <https://www.mail-archive.com/search?l=freesurfer%40nmr.mgh.harvard.edu&q=da…>Thread <https://www.mail-archive.com/search?l=freesurfer%40nmr.mgh.harvard.edu&q=su…>Billah, Tashrif <https://www.mail-archive.com/search?l=freesurfer%40nmr.mgh.harvard.edu&q=fr…> Right, I understand the rule about the scripts. However, my original question was about the subfields -hippocampal-subfields-T1/T2/T1T2 Again, can they be run with any of the autorecons separately? The example shown here<https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfields> integrates the subfileds with recon-all only but do no show combination with any autorecon commands. -Tashrif . From: Billah, Tashrif Sent: Friday, April 17, 2020 1:52 PM To: freesurfer(a)nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Which autorecon uses -hippocampal-subfields flags? Douglas, A little more elaboration would help. What is "it" and what are "them"? -Tashrif . ___ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer Re: [Freesurfer] Which autorecon uses -hippocampal-subfields flags? <https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg65827.html> 2020-04-17 <https://www.mail-archive.com/search?l=freesurfer%40nmr.mgh.harvard.edu&q=da…>Thread <https://www.mail-archive.com/search?l=freesurfer%40nmr.mgh.harvard.edu&q=su…>Douglas N. Greve <https://www.mail-archive.com/search?l=freesurfer%40nmr.mgh.harvard.edu&q=fr…> You have to run recon-all all the way through and then run the subfield scripts separately. On 4/17/2020 12:21 PM, Douglas N. Greve wrote: None! You have to run it all the way through to the end and then run them from the command line. On 4/17/2020 11:40 AM, Billah, Tashrif wrote: Hi all, Which of the three autorecons makes use of https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfields flags<https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfields%C2%A0flags>? autorecon1, 2 , or 3? My goal is to use the flag specifically with one of the three and not with recon-all in general as shown in the above page. I do understand that the new version of the commands are https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfieldsAndNucleiOfAm… Best, Tashrif ___ 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 Re: [Freesurfer] Which autorecon uses -hippocampal-subfields flags? <https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg65825.html> 2020-04-17 <https://www.mail-archive.com/search?l=freesurfer%40nmr.mgh.harvard.edu&q=da…>Thread <https://www.mail-archive.com/search?l=freesurfer%40nmr.mgh.harvard.edu&q=su…>Billah, Tashrif <https://www.mail-archive.com/search?l=freesurfer%40nmr.mgh.harvard.edu&q=fr…> Douglas, A little more elaboration would help. What is "it" and what are "them"? -Tashrif . ___ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer Re: [Freesurfer] Which autorecon uses -hippocampal-subfields flags? <https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg65818.html> 2020-04-17 <https://www.mail-archive.com/search?l=freesurfer%40nmr.mgh.harvard.edu&q=da…>Thread <https://www.mail-archive.com/search?l=freesurfer%40nmr.mgh.harvard.edu&q=su…>Douglas N. Greve <https://www.mail-archive.com/search?l=freesurfer%40nmr.mgh.harvard.edu&q=fr…> None! You have to run it all the way through to the end and then run them from the command line. On 4/17/2020 11:40 AM, Billah, Tashrif wrote: Hi all, Which of the three autorecons makes use of https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfields flags<https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfields%C2%A0flags>? autorecon1, 2 , or 3? My goal is to use the flag specifically with one of the three and not with recon-all in general as shown in the above page. I do understand that the new version of the commands are https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfieldsAndNucleiOfAm… Best, Tashrif ___ 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] Which autorecon uses -hippocampal-subfields flags? <https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg65814.html> 2020-04-17 <https://www.mail-archive.com/search?l=freesurfer%40nmr.mgh.harvard.edu&q=da…>Thread <https://www.mail-archive.com/search?l=freesurfer%40nmr.mgh.harvard.edu&q=su…>Billah, Tashrif <https://www.mail-archive.com/search?l=freesurfer%40nmr.mgh.harvard.edu&q=fr…> Hi all, Which of the three autorecons makes use of https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfields flags? autorecon1, 2 , or 3? My goal is to use the flag specifically with one of the three and not with recon-all in general as shown in the above page. I do understand that the new version of the commands are https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfieldsAndNucleiOfAm… Best, Tashrif ___ 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

2 1

Re: [Freesurfer] Which autorecon uses -hippocampal-subfields flags?
by Billah, Tashrif 01 May '20

01 May '20

[Freesurfer] Which autorecon uses -hippocampal-subfields flags?<https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg65836.html> 2020-04-17<https://www.mail-archive.com/search?l=freesurfer%40nmr.mgh.harvard.edu&q=da…> Thread<https://www.mail-archive.com/search?l=freesurfer%40nmr.mgh.harvard.edu&q=su…> Billah, Tashrif<https://www.mail-archive.com/search?l=freesurfer%40nmr.mgh.harvard.edu&q=fr…> Douglas, Let's try with an example. See the two ways T2 image can be integrated with recon-all Altogether: recon-all -subject subjectname -i /path/to/input_volume -T2 /path/to/T2_volume -T2pial -all autorecon3 only: recon-all -subject subjectname -T2 /path/to/T2_volume -T2pial -autorecon3 Similar to the former, -hippocampal-subfields-T1 integrated with recon-all: recon-all -all -s bert -hippocampal-subfields-T1 Now the question, compared to the latter, which autorecon[1/2/3] would accept -hippocampal-subfields-T1? Does it make sense now? -Tashrif . ___ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer Re: [Freesurfer] Which autorecon uses -hippocampal-subfields flags?<https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg65832.html> 2020-04-17<https://www.mail-archive.com/search?l=freesurfer%40nmr.mgh.harvard.edu&q=da…> Thread<https://www.mail-archive.com/search?l=freesurfer%40nmr.mgh.harvard.edu&q=su…> Douglas N. Greve<https://www.mail-archive.com/search?l=freesurfer%40nmr.mgh.harvard.edu&q=fr…> I don't understand the question. To run recon-all through to the end implies that you have run all the -autorecons On 4/17/2020 2:53 PM, Billah, Tashrif wrote: Right, I understand the rule about the scripts. However, my original question was about the subfields -hippocampal-subfields-T1/T2/T1T2 Again, can they be run with any of the autorecons separately? The example shown here <https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfields> integrates the subfileds with recon-all only but do no show combination with any autorecon commands. -Tashrif . *From:* Billah, Tashrif *Sent:* Friday, April 17, 2020 1:52 PM *To:* freesurfer(a)nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] Which autorecon uses -hippocampal-subfields flags? Douglas, A little more elaboration would help. What is "it" and what are "them"? -Tashrif . ___ 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 Re: [Freesurfer] Which autorecon uses -hippocampal-subfields flags?<https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg65829.html> 2020-04-17<https://www.mail-archive.com/search?l=freesurfer%40nmr.mgh.harvard.edu&q=da…> Thread<https://www.mail-archive.com/search?l=freesurfer%40nmr.mgh.harvard.edu&q=su…> Billah, Tashrif<https://www.mail-archive.com/search?l=freesurfer%40nmr.mgh.harvard.edu&q=fr…> Right, I understand the rule about the scripts. However, my original question was about the subfields -hippocampal-subfields-T1/T2/T1T2 Again, can they be run with any of the autorecons separately? The example shown here<https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfields> integrates the subfileds with recon-all only but do no show combination with any autorecon commands. -Tashrif . From: Billah, Tashrif Sent: Friday, April 17, 2020 1:52 PM To: freesurfer(a)nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Which autorecon uses -hippocampal-subfields flags? Douglas, A little more elaboration would help. What is "it" and what are "them"? -Tashrif . ___ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer Re: [Freesurfer] Which autorecon uses -hippocampal-subfields flags?<https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg65827.html> 2020-04-17<https://www.mail-archive.com/search?l=freesurfer%40nmr.mgh.harvard.edu&q=da…> Thread<https://www.mail-archive.com/search?l=freesurfer%40nmr.mgh.harvard.edu&q=su…> Douglas N. Greve<https://www.mail-archive.com/search?l=freesurfer%40nmr.mgh.harvard.edu&q=fr…> You have to run recon-all all the way through and then run the subfield scripts separately. On 4/17/2020 12:21 PM, Douglas N. Greve wrote: None! You have to run it all the way through to the end and then run them from the command line. On 4/17/2020 11:40 AM, Billah, Tashrif wrote: Hi all, Which of the three autorecons makes use of https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfields flags? autorecon1, 2 , or 3? My goal is to use the flag specifically with one of the three and not with recon-all in general as shown in the above page. I do understand that the new version of the commands are https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfieldsAndNucleiOfAm… Best, Tashrif ___ 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 Re: [Freesurfer] Which autorecon uses -hippocampal-subfields flags?<https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg65825.html> 2020-04-17<https://www.mail-archive.com/search?l=freesurfer%40nmr.mgh.harvard.edu&q=da…> Thread<https://www.mail-archive.com/search?l=freesurfer%40nmr.mgh.harvard.edu&q=su…> Billah, Tashrif<https://www.mail-archive.com/search?l=freesurfer%40nmr.mgh.harvard.edu&q=fr…> Douglas, A little more elaboration would help. What is "it" and what are "them"? -Tashrif . ___ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer Re: [Freesurfer] Which autorecon uses -hippocampal-subfields flags?<https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg65818.html> 2020-04-17<https://www.mail-archive.com/search?l=freesurfer%40nmr.mgh.harvard.edu&q=da…> Thread<https://www.mail-archive.com/search?l=freesurfer%40nmr.mgh.harvard.edu&q=su…> Douglas N. Greve<https://www.mail-archive.com/search?l=freesurfer%40nmr.mgh.harvard.edu&q=fr…> None! You have to run it all the way through to the end and then run them from the command line. On 4/17/2020 11:40 AM, Billah, Tashrif wrote: Hi all, Which of the three autorecons makes use of https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfields flags? autorecon1, 2 , or 3? My goal is to use the flag specifically with one of the three and not with recon-all in general as shown in the above page. I do understand that the new version of the commands are https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfieldsAndNucleiOfAm… Best, Tashrif ___ 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] Which autorecon uses -hippocampal-subfields flags?<https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg65814.html> 2020-04-17<https://www.mail-archive.com/search?l=freesurfer%40nmr.mgh.harvard.edu&q=da…> Thread<https://www.mail-archive.com/search?l=freesurfer%40nmr.mgh.harvard.edu&q=su…> Billah, Tashrif<https://www.mail-archive.com/search?l=freesurfer%40nmr.mgh.harvard.edu&q=fr…> Hi all, Which of the three autorecons makes use of https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfields flags? autorecon1, 2 , or 3? My goal is to use the flag specifically with one of the three and not with recon-all in general as shown in the above page. I do understand that the new version of the commands are https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfieldsAndNucleiOfAm… Best, Tashrif ___ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

2 1

ASEG and FAST Cerebellar Segmentations
by Camille Williams 01 May '20

01 May '20

External Email - Use Caution Hi, I am currently using data from the UKBiobank (https://www.ukbiobank.ac.uk/ <https://www.ukbiobank.ac.uk/>) which has segmented its brain imaging data using Freesurfer tools (https://biobank.ctsu.ox.ac.uk/crystal/crystal/docs/brain_mri.pdf <https://biobank.ctsu.ox.ac.uk/crystal/crystal/docs/brain_mri.pdf>). I calculated the sum of the FAST cerebellar grey matter volumes and compared them to the sum of the ASEG cerebellar cortex volumes. I only found a correlation around 75%. When I adjust both of these measures for TBV (Total Brain Volume, covariate method) and proceed to testing if there are sex effects in total cerebellar grey matter using linear regression, my results show that cerebellar volume is much larger in females than males when using the sum of the available FAST grey matter cerebellar volumes, and when I use the sum of the cerebellar cortex volumes provided by ASEG it appears that males have a much larger cerebellar cortex than females. Any thoughts as to why there is such a big discrepancy between segmentations ? Kind regards, Camille Williams PhD Candidate Laboratoire de Sciences Cognitives et Psycholinguistique (LSCP) Département d’Études en Sciences Cognitives École Normale Supérieure, Paris, France

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Error in mris_compute_lgi
by 肖伏龙 01 May '20

01 May '20

External Email - Use Caution hi all When I used the command "mris_compute_lgi --i lh.pial", there is an error which shows as followings: so how to solve this problem? Thank you very much!

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Ubuntu VM password
by Alex Mihai 01 May '20

01 May '20

External Email - Use Caution Hi guys! I have followed the virtual machine setup for virtual box freesurfer installation.but it ask me the password for the developer account. Which is the password? Cheers, Alex

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trac-all -bedp error
by Zeng, Qi 30 Apr '20

30 Apr '20

External Email - Use Caution Hi, I run trac-all, the log file has the following endings. "Queuing post processing stage" or "Queuing post processing stage 59 slices processed All slices processed /hpc/packages/minerva-common/freesurfer/6.0.0/freesurfer/bin/bedpostx_mgh: line 345: kill: (100952) - No such process". However, all outputs described in FSL BedpostX are generated dmri/FA, MD, V1, V2, V3 dmri.bedpostX/merged,mean,dyads, nodif_brain_mask Should I consider them as completed and move forward with -path? Best, Qi -- Ph.D. candidate Icahn School of Medicine at Mount Sinai

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