Freesurfer

freesurfer@nmr.mgh.harvard.edu

16 participants
30084 discussions

The cvs_avg35
by バキット・ムダシル 16 Apr '21

16 Apr '21

External Email - Use Caution Hi, I was looking for any document describes how the cvs_avg35 and cvs_avg35_inMNI152 were made? Can you please send me a link or give me a brief about it please? I searched in the freesurfer wiki and here in the freesurfer folder but no success. Also, I found from literature that the fsaverage was made from a data of 40 subjects that includes 10 cases of Alzheimer disease. Can I ask what was the reason to include those 10 cases to create this template? Thanks Mudathir

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euclidian distance masks using free surfer tools
by Ritobrato Datta 16 Apr '21

16 Apr '21

External Email - Use Caution Hello, I want to create 3-dimensional euclidean / geodesic distance masks that are essentially concentric rings of 3 mm thickness in the white matter that start from the ventricle toward the cortex. Is there an easy way to do that using freesurfer tools ? I have attached a figure from an article where this approach has been used. [image: Screen Shot 2021-04-15 at 11.38.15 AM.png] Please let me know. Thanks Ri

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Re: [Freesurfer] Surface registration problem
by Manenti, Giorgio 16 Apr '21

16 Apr '21

External Email - Use Caution Dear Greve, Thank you very much for your reply, yes indeed i found the problem which was connected to the deletion of 1 slice of the functional data in order to run the FSL "topup" b02b0.cnf flag. I solved it by changing this step, using the b02b0_2.cnf for odd number of slices. Many thanks again Best Giorgio

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Tract endpoint density map surface overlay
by バキット・ムダシル 16 Apr '21

16 Apr '21

External Email - Use Caution Hi everyone, I need to confirm if the steps below are correct, so I would like to ask freesurfer experts help. By using the Left-Cerebral-White-Matter mask imported from freesurfer as a seed I created a tract end points density image of the arcuate fasciculus in a NIFTI format (first figure). I want to display the image on the same subject’s white matter surface. So, I wrote the command as follows mri_vol2surf --src DensityMAP.nii.gz --out filename.mgh --hemi lh --surf white --out_type mgh --regheader subject_id The output as seen in the second figure. Thanks Mudathir

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Thalamic segmentation in FS voxel space
by Thomas, George 15 Apr '21

15 Apr '21

External Email - Use Caution Dear All, I have run segmentThalamicNuclei.sh on a set of subjects with 1mm isotropic T1 images. I need to convert these labels into volumetric space for further analysis so have been using the output with the FSvoxelSpace suffix and converting .mgz to .nii using mri_convert However, for some of the subnuclei there seems to be a large discrepancy between the surface-based volumetric measurement completed by quantifyThalamicNuclei.sh, and the number of voxels in the FSvoxelSpace output. Across the whole dataset of ~130 subjects, the left and right VM nuclei have a mean volume of about 25mm^3 according to quantifyThalamicNuclei.sh but are only represented by about 2-3 voxels per subject in the FSvoxelSpace output and are sometimes absent entirely. I have found this to be similar for the VAmc (~30mm^3) and CL nuclei (~40mm^3), both of which are represented many fewer voxels than one might expect (~6 and ~20 voxels, respectively). Of course, it will not always be possible to represent a given surface in voxel-space and you would expect some differences but am wondering why the discrepancy might be so large in these cases, and if there is anything that might be done to remedy this? Many thanks, George Thomas

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Failed tissue type check {Disarmed}
by Julie Ottoy 15 Apr '21

15 Apr '21

External Email - Use Caution Dear Doug, I have the same issue as the people below. I was wondering if this was solved in the meantime. I ran petsurfer gtmpvc with the psf 0 and no-tfe flags to not do PVC and got the following error in only one of my subjects. When I ran the same subject with PVC and specified psf, it did run fine. $Id: mri_gtmpvc.c,- setenv - cd - mri_gtmpvc --i /input.nii.gz --reg PET.lta --psf 0 --no-tfe --seg gtmseg.mgz --default-seg-merge --auto-mask 10 0.01 --mgx 0.01 --o /gtmnopvc.output.ceregrey --rescale 8 47 sysname Linux hostname - machine - user - vgthresh 0.001000 nReplace 18 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 24 avail.processors, using 1 Creating output directory /gtmnopvc.output.ceregrey Loading seg for gtm /ID/mri/gtmseg.mgz Loading seg ctab /ID/mri/gtmseg.ctab Reading /ID/mri/gtmseg.lta Replacing 18 Pruning ctab Checking tissue type ERROR: CheckSegTissueType() tissue type for seg 29 Left-undetermined not set Failed tissue type check Any suggestions would be appreciated! Thank you, Julie Re: [Freesurfer] mri_gtmpvc error: failed tissue type check <https://secure-web.cisco.com/1-AfjZga-sPrQL2DD6_knJ0CVtb1mQnm-139FdXZgREjGD…> 2017-11-25 <https://secure-web.cisco.com/1wmX-yI5dbw4l_pxYy3eoVUJqMBCtBczIUKuXvmoQaLof8…> Thread <https://secure-web.cisco.com/1H-6HNMBxeDbZPyhVbOH9A2eLQckCsYtW7MQ3G9W6kDVwa…> Douglas Greve <https://secure-web.cisco.com/1WfAMB3Ad9t1D_s6Buw38joSkwdCcFg-F8c6cN0W9n84zV…> sorry, can you send me the details again? On 11/21/17 10:24 AM, Klein, Gregory wrote: Hello Donatas and Douglas, Did you ever find a cause and solution for this problem? I too occasionally get this error message, and cannot get the results of mri_gtmpvc for certain subjects. Any suggestions are welcome. Thanks, Greg -- Gregory Klein, PhD Principal Scientist, Biomarker Experimental Medicine Leader F. Hoffmann-La Roche Ltd. Bldg 01, Floor 16, N445 Grenazacherstrasse 170, 4070 Basel, Switzerland Mobile: +41 79 572 97 89 Office Phone: +41 61 682 07 59 email: gregory.kl...(a)roche.com Roche Products Limited, 6 Falcon Way, Shire Park, Welwyn Garden City, AL7 1TW Registration No:100674 Confidentiality note: This message is intended for the use of the named recipient(s) only and may contain confidential and / or privileged information. If you are not the intended recipient, please contact the sender and delete this message. Any unauthorized use of the information contained in this message is prohibited. ___ Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://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 athttp://http://secure-web.cisco.com/1Kuqledw2eJViDlbH8MA0_r7jBLVXWD3VreLVX… . 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. Re: [Freesurfer] mri_gtmpvc error: failed tissue type check <https://secure-web.cisco.com/1vNIDvkxU5C3l-uZggX6Oz-MWAWokjyVkJCUVlEhq9XKRo…> 2016-11-09 <https://secure-web.cisco.com/1VugCXXwalKKVT7bLxwwxB0wUwO_LQ0hZG5P6oNAE9_RkA…> Thread <https://secure-web.cisco.com/1H-6HNMBxeDbZPyhVbOH9A2eLQckCsYtW7MQ3G9W6kDVwa…> Douglas N Greve <https://secure-web.cisco.com/1M-leUu9vjxLEhQIgnl6dfbF3d7ST4-ULxvVl3JoB7UDa6…> Donatas, please remember to include previous correspondence so that we have everything in one email. Can you upload your freesurfer subject so that I can debug it further? upload to https://secure-web.cisco.com/1IYyWkyzVzqvMHe5CQVU03U4UqcuGDMK5jId9qWFaW81r6… On 11/09/2016 12:17 PM, Donatas Sederevicius wrote: > > I followed the processing workflow as described in PETSurfer wiki > and gtmseg.mgz was created using gtmseg script as described. I > ran this processing for over 100 subjects and only one has failed. > > > > ___ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://secure-web.cisco.com/1Aj-KIXWBSRBh4QYhiT5lPQzukbBDpNzMoSUI14TDJiN4-… -- Douglas N. Greve, Ph.D. MGH-NMR Centergr...(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://secure-web.cisco.com/1ThbUNbSt9_UBVJvAmBRnAaRfVWyZ0ej5JxRkdyy8xuH36… Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://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 athttp://http://secure-web.cisco.com/1Kuqledw2eJViDlbH8MA0_r7jBLVXWD3VreLVX… . 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. Re: [Freesurfer] mri_gtmpvc error: failed tissue type check <https://secure-web.cisco.com/1yv39xApOHJ3FS6xDcFycnMnbHtStZeNBiLl3QzfL8G4yu…> 2016-11-09 <https://secure-web.cisco.com/1VugCXXwalKKVT7bLxwwxB0wUwO_LQ0hZG5P6oNAE9_RkA…> Thread <https://secure-web.cisco.com/1H-6HNMBxeDbZPyhVbOH9A2eLQckCsYtW7MQ3G9W6kDVwa…> Donatas Sederevicius <https://secure-web.cisco.com/1JNZMWhSBxxqZ4whfRrQXZBTWg88CVAVN7kKCidcLVIRKl…> I followed the processing workflow as described in PETSurfer wiki and gtmseg.mgz was created using gtmseg script as described. I ran this processing for over 100 subjects and only one has failed. ___ Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://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 athttp://http://secure-web.cisco.com/1Kuqledw2eJViDlbH8MA0_r7jBLVXWD3VreLVX… . 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. Re: [Freesurfer] mri_gtmpvc error: failed tissue type check <https://secure-web.cisco.com/1vPxlf-9EcToYjQ2NcohNFPvheryGJhjZq4nxdkmbOKRg2…> 2016-11-09 <https://secure-web.cisco.com/1VugCXXwalKKVT7bLxwwxB0wUwO_LQ0hZG5P6oNAE9_RkA…> Thread <https://secure-web.cisco.com/1H-6HNMBxeDbZPyhVbOH9A2eLQckCsYtW7MQ3G9W6kDVwa…> Douglas Greve <https://secure-web.cisco.com/1WfAMB3Ad9t1D_s6Buw38joSkwdCcFg-F8c6cN0W9n84zV…> Was gtmseg.mgz created with the gtmseg script? On 11/9/16 4:43 AM, Donatas Sederevicius wrote: Dear Freesurfer community, An error has occured while applying PET partial volume correction using mri_gtmpvc. A snippet from the log file: Reading /projects/PET/recon/ID247/mri/gtmseg.lta Replacing 18 ERROR: CheckSegTissueType() tissue type for seg 29 Left-undetermined not set Failed tissue type check gtmseg was run as: gtmseg --s ID247 and completed without errors. mri_gtmpvc was run as: mri_gtmpvc --i /projects/PET/processed/ID247/ID247_PIBStatic.nii.gz --psf 2 --no-rescale --seg /projects/PET/recon/ID247/mri/gtmseg.mgz --reg /projects/PET/processed/ID247/PET2MRI.lta --default-seg-merge --o /projects/PET/processed/ID247/gtmpvcYES.output/SGTM/non_scaled --save-input --km-ref 8 47 --km-hb 11 12 13 50 51 52 How could this problem be solved? Thank you. Best regards, Donatas ___ Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://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 athttp://http://secure-web.cisco.com/1Kuqledw2eJViDlbH8MA0_r7jBLVXWD3VreLVX… . 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] mri_gtmpvc error: failed tissue type check <https://secure-web.cisco.com/1-KTvEDdAuFhtSF_p9XP0T2HYXV7p_VXGloR253IuV-slW…> 2016-11-09 <https://secure-web.cisco.com/1VugCXXwalKKVT7bLxwwxB0wUwO_LQ0hZG5P6oNAE9_RkA…> Thread <https://secure-web.cisco.com/1H-6HNMBxeDbZPyhVbOH9A2eLQckCsYtW7MQ3G9W6kDVwa…> Donatas Sederevicius <https://secure-web.cisco.com/1JNZMWhSBxxqZ4whfRrQXZBTWg88CVAVN7kKCidcLVIRKl…> Dear Freesurfer community, An error has occured while applying PET partial volume correction using mri_gtmpvc. A snippet from the log file: Reading /projects/PET/recon/ID247/mri/gtmseg.lta Replacing 18 ERROR: CheckSegTissueType() tissue type for seg 29 Left-undetermined not set Failed tissue type check gtmseg was run as: gtmseg --s ID247 and completed without errors. mri_gtmpvc was run as: mri_gtmpvc --i /projects/PET/processed/ID247/ID247_PIBStatic.nii.gz --psf 2 --no-rescale --seg /projects/PET/recon/ID247/mri/gtmseg.mgz --reg /projects/PET/processed/ID247/PET2MRI.lta --default-seg-merge --o /projects/PET/processed/ID247/gtmpvcYES.output/SGTM/non_scaled --save-input --km-ref 8 47 --km-hb 11 12 13 50 51 52 How could this problem be solved? Thank you. Best regards, Donatas ___ Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://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 athttp://http://secure-web.cisco.com/1Kuqledw2eJViDlbH8MA0_r7jBLVXWD3VreLVX… . 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] Subthalamic nucleus volume (Douglas N. Greve)
by T. Pansuwan 15 Apr '21

15 Apr '21

External Email - Use Caution Dear Douglas, Thank you for your reply. Could you possibly elaborate more on how this method will only reflect the registration in that area instead of volume? I got this method from freesurfer tutorial on obtaining custom anatomical ROI analysis. And do you have any suggestion on an alternative method to accurately obtain sub thalamic nucleus volume? Best wishes, Tanrada On 5 Apr 2021, at 17:00, freesurfer-request(a)nmr.mgh.harvard.edu<mailto:freesurfer-request@nmr.mgh.harvard.edu> wrote: Send Freesurfer mailing list submissions to freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu> To subscribe or unsubscribe via the World Wide Web, visit https://secure-web.cisco.com/1PnvGdDTvGiiuryCfCtkEyKZ_3eFX0083pdxmuvq9ozNFT… or, via email, send a message with subject or body 'help' to freesurfer-request(a)nmr.mgh.harvard.edu You can reach the person managing the list at freesurfer-owner(a)nmr.mgh.harvard.edu When replying, please edit your Subject line so it is more specific than "Re: Contents of Freesurfer digest..." Today's Topics: 1. Dicom Tag Problem Reconall (Banu Femir) 2. mri_vol2surf empty output (Karan Desai) 3. mri_gtmpvc error Checking tissue type ERROR: CheckSegTissueType() tissue type for seg (Bahar Hazal Yal??nkaya) 4. Re: make_average_subject error (Douglas N. Greve) 5. Re: Running recon-all with FLAIR (Douglas N. Greve) 6. Re: functional to anatomical registration question (Douglas N. Greve) 7. Re: Problem with freesurfer measures (Douglas N. Greve) 8. Re: ERROR: Cannot find stats file (Douglas N. Greve) 9. Re: Subthalamic nucleus volume (Douglas N. Greve) 10. Re: Talairach Failed: Distorted T1 (Douglas N. Greve) 11. Re: quantification of volume of perivascular spaces (Douglas N. Greve) 12. "ERROR: crypt() returned null with 4-line file" (Cook, Philip) 13. Re: Problem with freesurfer measures (Alberto Del Cerro Leon) ---------------------------------------------------------------------- Message: 1 Date: Sun, 4 Apr 2021 22:57:57 +0300 From: Banu Femir <banu.femir(a)gmail.com> Subject: [Freesurfer] Dicom Tag Problem Reconall To: freesurfer(a)nmr.mgh.harvard.edu Message-ID: <CANuRgTpGaqjYJVd9V+n3-82ASsx0uP=S=3dH5ksxoxda34S3gA(a)mail.gmail.com> Content-Type: text/plain; charset="utf-8" External Email - Use Caution Dear Freesurfer Developers, I'm trying to analyze a set of MRI data that I got via CD. Dicom files did not have .dcm extension, so I used a program and they turned into a .dcm image. My reconall run for around 2 hours, after I got an error: Counting frames nframes = 481 nslices = 1 ndcmfiles = 481 PE Dir = UNKNOWN (dicom read) Loading pixel data JPEG compressed, decompressing cd /home/banu/usr/local/freesurfer/subjects/sepsis1dicomwritebelow fsdcmdecompress --i /home/banu/Documents/Sepsis/yeni_dicom_write_below/F_000001.dcm --o /tmp/banu.tmp.decompressed.dcm.1TXZUy --jpeg >& /tmp/banu.tmp.decompressed.dcm.1TXZUy.dcmdjpeg.out ERROR: 512, see /tmp/banu.tmp.decompressed.dcm.1TXZUy.dcmdjpeg.out for more details Linux banuf 4.15.0-51-generic #55-Ubuntu SMP Wed May 15 14:27:21 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux Before that, I got many Warnings about imagenumber, tag serial number, seriesnumber, tag, ect. In case you want I can share the whole log file. I am wondering if there was sth wrong with my .dcm format. If yes, how I can solve this problem? It seems like there was sth wrong with tags, but I really cannot solve the problem. Many thanks! Have a nice and healthy week! Banu

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mri_segstats to report empty and non-empty segmentation
by miracle ozzoude 15 Apr '21

15 Apr '21

External Email - Use Caution Hello Experts, I am using mri_segstats with the --ctab flag to extract dti and suvr values from a white matter hyperintensities parcellation. Running mri_segstats on the image and parcellation with --ctab only reports on non-empty segmentations. I want it to also report on the empty segmentations. Is there a flag or any other freesurfer commands that i can use? Summary: I want mri_segstats to report on non-empty and empty segmentations, not just the former. Cheers. cmdline mri_segstats --seg wmh_lobar.nii.gz --i subj_rescaled_wholecere_PET2T1_smooth.nii.gz --sum SUVR_WMH_lobar.stats --ctab WMColorLUT.ctab --pv norm.mgz Loading wmh_lobar.nii.gz INFO: using NIfTI-1 qform Loading subj_rescaled_wholecere_PET2T1_smooth.nii.gz Loading norm.mgz Voxel Volume is 1 mm^3 Generating list of segmentation ids Found 13 segmentations Computing statistics for each segmentationReporting on 11 segmentations Using PrintSegStat mri_segstats done

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mkcontrast2 typo in 7.1.1
by Ben Singer 15 Apr '21

15 Apr '21

External Email - Use Caution On line 106: if($FS_MKCON_USE_BIN == 0 && UseOctave == 0) then there should be a "$" before the "UseOctave" to make the line read: if($FS_MKCON_USE_BIN == 0 && $UseOctave == 0) then Apologies if this has been already corrected, I didn't come across this in an archive search. It looks like this bug originated in July 2018, and is the reason for a few 2019 and one or two 2020 posts complaining of "MATLAB: variable undefined" errors. Below here is just some more background info about what sort of errors might result, and why setting the MATLAB variable to the matlab executable works around the problem, but causes a new problem with the mex command. The conditional is always false before the fix-- so the MATLAB variable is never set to whatever fsfast's "getmatlab" function assigns to it, in the body of the conditional. So this could be the source of several "MATLAB: Undefined variable" errors reported on this list. If one sets the MATLAB environment variable to the "R20xx/bin/matlab" executable , one can work around this problem. But-- the Matlab "mex" command uses the MATLAB variable, and expects it to be set to the Matlab root directory in order to determine the machine architecture for your host (type "mex" at the shell prompt when MATLAB is set to the matlab executable, to see the error message.) Setting the MATLAB variable the way the "mex" command expects would then result in "/path/to/R20xx: permission denied" errors when running mkcontrast-related scripts. Sorry for the wordiness. Bottom line is dollar sign.

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aparc+aseg to native space issue
by Larson, Kathleen E 15 Apr '21

15 Apr '21

External Email - Use Caution Hi, I am having an issue converting the aparc+aseg segmentation into the native space. I have tried using both of the following commands: mri_label2vol --seg aparc+aseg.mgz --temp rawavg.mgz --o aparc+aseg_native.mgz --regheader mri_vol2vol --mov aparc+aseg.mgz --targ rawavg.mgz --regheader --nearest --o aparc+aseg_native.mgz In both cases, the output segmentation in native space is slightly offset along the x axis (given x,y,z coordinates). In fact, mri_label2vol is offset in the opposite direction as mri_vol2vol. All outputs have the same origin as the original native space, so I am wondering if it's a problem with the interpolation. Do you have any advice for how to fix this issue? Thank you! Kathleen Larson (she/her) Medical Image Computing Lab (MedICL) Biomedical Engineering | Ph.D. Candidate Vanderbilt University

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