Freesurfer

freesurfer@nmr.mgh.harvard.edu

12 participants
30081 discussions

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

2 2

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

2 1

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.

3 10

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

2 1

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

2 1

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.

2 1

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

2 2

Surface registration problem
by Manenti, Giorgio 15 Apr '21

15 Apr '21

External Email - Use Caution Dear Experts, I’m encountering a problem when running the preproc-sess on my functional data. When using the flag -surface subject hemi i am getting ":ERROR: source volume is neither source nor target of the registration”. The source is a template.nii file present in the bold folders, while the destination file is the mri/orig.mgz from the “subject” folder (after Longitudinal recon-all). I am not sure if the problem could be connected with the mc-sess,stc-sess or topup (where i need to crop out 1 slice to get an even volume) steps, that i’m running before preproc-sess, or if i’m missing an extra flag. Here the command i’m running: preproc-sess -s f10_sess01new -fsd bold -i my_hifi_images -nostc -nomc -surface hum_15721.long.long010 lhrh -mni305 -fwhm 4 -per-run Many thanks for your time and support, Best Regards Giorgio

2 1

Re: [Freesurfer] Freesurfer Digest, Vol 206, Issue 6
by zalewk 15 Apr '21

15 Apr '21

External Email - Use Caution Hi Doug, Sorry for the late reply, and thanks for all your help. Attached is the text file of the output. This was testing autorecon-pial, but the bug is the same no matter if it's autorecon2-wm, autorecon3, or any place it hits the "if ( $ud" statement. Best, Kody Run it with -debug as the first option, capture the output, and send it to us. On 4/1/2021 8:29 PM, zalewk wrote: > > ????????External Email - Use Caution > > Hi Freesurfer team, > > My lab recently switched over from FS6 to FS7 and I think I've > encountered a bug with recon-all. > I'm running subjects stepwise and editing them, running recon-all with > the -autorecon2 and -autorecon3 flags initially are no problem, they > run fine.? Trying to re-run them or use the -autorecon2-wm, > -autorecon-pial etc. flags lead to crashing at certain parts of the > program. The error message I get is "if: expression syntax". Digging > into the code, it seems to crash when it hits a line of code "if($ud > || $ForceUpdate)". The syntax superficially looks right (I don't know > tcsh), checking the variables it seems like $ForceUpdate is never set, > but removing it from recon-all doesn't fix the problem. > It seems the $ud variable is for checking if updates are needed for a > set of volumes passed to the program. I don't know why that would be a > problematic argument, removing that part seems to fix it, but this > also seems like an important variable and I don't know enough about > tcsh to understand why it works after removing it. Can one of the > folks who wrote the recon-all script help me out? I'm running the > commands step-wise as a work-around, but that is much less convenient. > > Best, ________________________________ From: freesurfer-bounces(a)nmr.mgh.harvard.edu <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of freesurfer-request(a)nmr.mgh.harvard.edu <freesurfer-request(a)nmr.mgh.harvard.edu> Sent: Tuesday, April 6, 2021 6:41 AM To: freesurfer(a)nmr.mgh.harvard.edu <freesurfer(a)nmr.mgh.harvard.edu> Subject: Freesurfer Digest, Vol 206, Issue 6 Send Freesurfer mailing list submissions to freesurfer(a)nmr.mgh.harvard.edu To subscribe or unsubscribe via the World Wide Web, visit https://secure-web.cisco.com/12RCdM4nvnTq08RfLMdhWLNUwwCLn6K8WftCJlAbuQ-Iak… 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. Freesurfer Website Ports (Swearingen, Hannah) 2. mris_average_surface fails (?????????) 3. Re: 2mm thick image for hippocampal segmentation. (Ramesh Babu) 4. Re: fMRIPrep BOLD Output (Douglas N. Greve) 5. Re: mri_glmfit error (Douglas N. Greve) 6. Re: Regarding recon all (Douglas N. Greve) 7. Re: retaining label ids (Douglas N. Greve) 8. Re: recon-all bug (Douglas N. Greve) 9. Re: mris_label2annot - make all command exiting with errors (Douglas N. Greve) 10. Re: recon-all bug (Douglas N. Greve) 11. Re: Dicom Tag Problem Reconall (Douglas N. Greve) 12. unsubscribe (Coleman, Katherine) 13. Re: mri_gtmpvc error Checking tissue type ERROR: CheckSegTissueType() tissue type for seg (Douglas N. Greve) 14. Re: Problem with freesurfer measures (Douglas N. Greve) 15. Re: Freesurfer Website Ports (Douglas N. Greve) 16. Re: mris_average_surface fails (Douglas N. Greve) 17. Re: 2mm thick image for hippocampal segmentation. (Douglas N. Greve) 18. Freesurfer Versions - Zeros in the Cortex (Daniel Gutstein) 19. Re: mri_gtmpvc error Checking tissue type ERROR: CheckSegTissueType() tissue type for seg (Bahar Hazal Yal??nkaya) ---------------------------------------------------------------------- Message: 1 Date: Mon, 5 Apr 2021 15:20:31 -0400 From: "Swearingen, Hannah" <hannah_swearingen1(a)brown.edu> Subject: [Freesurfer] Freesurfer Website Ports To: freesurfer(a)nmr.mgh.harvard.edu Message-ID: <CAG+grQp1wJ8ywX0StrT4VJO38JYtwfxivTNvdH3KwQrhtwiRGw(a)mail.gmail.com> Content-Type: text/plain; charset="utf-8" External Email - Use Caution Hi, I am setting up an Access Control List for an isolated VLAN in which my center's neuroimaging computing workstations will be connected to our hospital's network for data back-up. We want to be able to connect to Freesurfer's website while connected to the VLAN, and we need to supply which ports the website accesses. I used nmap to scan and see which ports are open, and I found this: PORT STATE SERVICE 21/tcp open ftp 80/tcp open http 443/tcp open https Our hospital's IT is unsure if the FTP port can be opened without a security breach, and they are wondering if we will still be able to access the website without the 21/FTP port opened? Can anyone provide me with that information? Thanks, Hannah --

2 1

Decompressed problem during reconall
by Banu Femir 15 Apr '21

15 Apr '21

External Email - Use Caution Dear FreeSurfer Developers, I've a problem that cannot solve for the last week. I am using virtual box, FS7 on my windows. I run reconall for Bert and checked that it is working.I have an MRI scan of sepstic patients that I got via CD, these are DICOM files but does not end with .dcm. When I try to run reconall, for dcm images I got the following error (the longer version is in the attachment) ........ Loading pixel data JPEG compressed, decompressing cd /home/developer/Documents/7.1.0-1/subjects/sepsis2 fsdcmdecompress --i /home/developer/Documents/7.1.0-1/subjects/D_000001/F_000001 --o /tmp/developer.tmp.decompressed.dcm.0oOV4x --jpeg >& /tmp/developer.tmp.decompressed.dcm.0oOV4x.dcmdjpeg.out ERROR: 512, see /tmp/developer.tmp.decompressed.dcm.0oOV4x.dcmdjpeg.out for more details Command exited with non-zero status 1 @#@FSTIME 2021:04:08:08:29:16 mri_convert N 2 e 1.97 S 1.19 U 0.60 P 91% M 9200 F 2 R 999 W 0 c 174 w 356 I 32240 O 0 L 0.55 0.33 0.41 @#@FSLOADPOST 2021:04:08:08:29:18 mri_convert N 2 0.55 0.33 0.41 Linux developer-VirtualBox 5.3.0-53-generic #47~18.04.1-Ubuntu SMP Thu May 7 13:10:50 UTC 2020 x86_64 x86_64 x86_64 GNU/Linux recon-all -s sepsis2 exited with ERRORS at Thu Apr 8 08:29:18 EDT 202 I converted files to nii, this time I decided to run reconall on nii images, it took more time but again failed on talairach transform. I tried to run on different shells but ended up with the same problem. Is it related with my MRI data or computer, how can I understand that? Many thanks! Banu

2 1

Jump to page:

2026

2025

2024

2023

2022

2021

2020

2019

2018

2017

2016

2015

2014

2013

2012

2011

2010

2009

2008

2007

2006

2005

2004

Freesurfer