Freesurfer April 2021

freesurfer@nmr.mgh.harvard.edu

104 participants
144 discussions

2mm thick image for hippocampal segmentation.
by Ramesh Babu 06 Apr '21

06 Apr '21

External Email - Use Caution Dear Experts, For our project work, we particularly looking for hippocampal and its subfield volumes. Using GE 1.5T scanner, we tried a 3D BRAVO sequence with 1x1x1 resolution, 256x256x160 dimension with 8* flip angle which produced images with a lot of noise. Then we tried the same sequence with 1x1x2 resolution, and 256x256x80 FOV, which produced a clean image without noise. When we reformatted the images, it produces 0.5x0.5x1 resolution with 512x512x172 dimension. Is this sequence good for hippocampal volume estimation and subfield segmentation (also for whole-brain VBM analysis)? Could you please suggest to me a correct sequence for our project? Regards Ramesh

4 6

b0dc flag for Freesurfer7
by Manenti, Giorgio 06 Apr '21

06 Apr '21

External Email - Use Caution Dear Experts, I am wondering if there is additional documentation about the -b0dc flag for mkanalysis-sess. This flag is applying field distortion correction. Is it possible to use my topup information in order to correct it or it s a different field correction? Many thanks, Best Giorgio

2 1

Fwd: Failed tissue type check {Disarmed}
by Julie Ottoy 06 Apr '21

06 Apr '21

External Email - Use Caution Hi Doug, Did you have a chance to look at this subject ? Thanks a lot, Julie ---------- Forwarded message --------- From: Julie Ottoy <julie.jj.ottoy(a)gmail.com> Date: Thu, 18 Mar 2021 at 13:08 Subject: Re: [Freesurfer] Failed tissue type check {Disarmed} To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Hi Doug I upload the files on the server, see subject_ottoy.tar.gz thanks a lot! Julie On Tue, 16 Mar 2021 at 12:03, Douglas N. Greve <dgreve(a)mgh.harvard.edu> wrote: > I don't know. Can you upload the data so I can take a look? Instructions > are below. I'd need both the anatomical data (output of recon-all) and > input.nii.gz and PET.lta > > From the linux command line, > Create the file you want to upload, eg, > cd $SUBJECTS_DIR > tar cvfz subject.tar.gz ./subject > Now log into our anonymous FTP site: > ftp surfer.nmr.mgh.harvard.edu > It will ask you for a user name: use "anonymous" (no quotes) > It will ask you for a password: use "anonymous" (no quotes) > cd transfer/incoming > binary > put subject.tar.gz > Send an email that the file has been and the name of the file. > > > > On 3/8/2021 11:47 AM, Julie Ottoy wrote: > > External Email - Use Caution > Hi Doug, > > Any other suggestions I could try? It seems to be only an issue with the > non-pvc data. > > Thanks > Julie > > On Tue, 2 Feb 2021 at 11:10, Julie Ottoy <julie.jj.ottoy(a)gmail.com> wrote: > >> Hi Doug, >> >> I tried these fixes but they still give me the error message below. I did >> replace it in the gtmseg.ctab though -- should it be perhaps the seg.ctab >> in the aux folder ? >> >> Thanks, >> Julie >> >> On Tue, 12 Jan 2021 at 10:37, Julie Ottoy <julie.jj.ottoy(a)gmail.com> >> wrote: >> >>> Hi Doug >>> >>> I tried that as well but getting the same error as with --replace 29 3. >>> >>> ERROR: CTABpruneCTab(): ctab does not have segid 2 >>> >>> >>> Thanks, >>> julie >>> >>> On Tue, 12 Jan 2021 at 10:35, Greve, Douglas N.,Ph.D. < >>> DGREVE(a)mgh.harvard.edu> wrote: >>> >>>> Try using --replace 29 2 >>>> >>>> >>>> On 12/29/2020 12:48 PM, Julie Ottoy wrote: >>>> >>>> External Email - Use Caution >>>> Hi Doug >>>> >>>> Thanks for your reply. I tried both your suggestions, but it seems as >>>> though they both ran into an error. >>>> >>>> For your first suggestion, i.e. adding --replace 29 3 to the command >>>> line of gtmpvc, I get the error: >>>> >>>> Loading seg for gtm 057_S_5295re/mri/gtmseg.mgz >>>> >>>> Loading seg ctab 057_S_5295re/mri/gtmseg.ctab >>>> >>>> Reading 057_S_5295re/mri/gtmseg.lta >>>> >>>> Replacing 19 >>>> >>>> Pruning ctab >>>> >>>> ERROR: CTABpruneCTab(): ctab does not have segid 3 >>>> >>>> >>>> For your second suggestion, i.e. I replaced the following line in the >>>> ctab: >>>> >>>> 29 Left-undetermined 135 206 235 0 -1 >>>> >>>> ==> replaced by: 29 Left-undetermined 135 206 235 0 >>>> 3 >>>> >>>> >>>> I get the error: >>>> >>>> Computing Seg in input space >>>> >>>> Building GTM DoVoxFracCor=0 >>>> >>>> ERROR: creating region for nthseg=12, segid=29, Left-undetermined >>>> >>>> It may be that there are no voxels for this seg when mapped into the >>>> input space. >>>> >>>> Check 057_S_5295/057_S_5295.gtmnopvc.output.pons/aux/seg.nii.gz and the >>>> registration >>>> >>>> Build time 5.9690, err = 1 >>>> >>>> >>>> Thank you, >>>> >>>> Julie >>>> >>>> On Wed, 23 Dec 2020 at 12:48, Greve, Douglas N.,Ph.D. < >>>> DGREVE(a)mgh.harvard.edu> wrote: >>>> >>>>> You can use the fix from my previous email or you can add the >>>>> following line any were into the gtmseg.ctab file: >>>>> 29 Left-undetermined 135 206 235 0 3 >>>>> >>>>> >>>>> On 12/18/2020 11:06 PM, Julie Ottoy wrote: >>>>> >>>>> External Email - Use Caution >>>>> Sorry I would like to correct my previous post. The subject also >>>>> failed with PVC. >>>>> I see now that the issue is happening during the gtm seg stage where >>>>> it gives the error: WARNING: segid 29 Left-undetermined tissue type is >>>>> not set. >>>>> For your information: I ran the standard FS and petsurfer pipeline as >>>>> outlined on the wiki. I tried two gtm seg commands: >>>>> gtmseg --s ${id} --xcerseg --keep-hypo --subsegwm --subseg-cblum-wm >>>>> gtmseg --s ${id} --keep-cc --no-xcerseg --keep-hypo --subsegwm >>>>> --subseg-cblum-wm >>>>> >>>>> Thank you for your help, >>>>> Julie >>>>> >>>>> On Fri, 18 Dec 2020 at 00:09, Julie Ottoy <julie.jj.ottoy(a)gmail.com> >>>>> wrote: >>>>> >>>>>> 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(a)nmr.mgh.harvard.edu*MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://secure-web.cisco.com/1sA96g6MVXhTKqyIohE7iDpAeVudtNSoraQRr6PoymCFS6… <https://secure-web.cisco.com/1Aj-KIXWBSRBh4QYhiT5lPQzukbBDpNzMoSUI14TDJiN4-…> >>>>>> >>>>>> >>>>>> 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*MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* http://secure-web.cisco.com/1pcd3R17cw9CUmO-RFZqcKXMAKlR9Hi_f5yRd0WcMyKMI2V… <http://secure-web.cisco.com/1Kuqledw2eJViDlbH8MA0_r7jBLVXWD3VreLVXqKwRqHFX1…> . 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 >>>>>> >>>>>> *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://secure-web.cisco.com/1eGgq3MtUZinN6YC13LiaDErXWJN9vgi9QwYQxtVWBl6Ea… <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 >>>>>> > *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://secure-web.cisco.com/1sA96g6MVXhTKqyIohE7iDpAeVudtNSoraQRr6PoymCFS6… <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 <http://secure-web.cisco.com/18hglveD2QhtSJ7bQFM9F3sXBln9p2f7eLtue0lnyouc5FB…> >>>>>> FileDrop: *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://secure-web.cisco.com/1eGgq3MtUZinN6YC13LiaDErXWJN9vgi9QwYQxtVWBl6Ea… <https://secure-web.cisco.com/1IYyWkyzVzqvMHe5CQVU03U4UqcuGDMK5jId9qWFaW81r6…>*MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* http://secure-web.cisco.com/1En2sExPLORX4J1w9LZmBmOFgR3GA3uFmBVMOMf2e7NMCyv… <http://secure-web.cisco.com/19vdC8-giAFd6ifd70PmXkEzKNFxO_PL9uIhgUKTBRjgXJM…> >>>>>> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ >>>>>> >>>>>> ___ >>>>>> Freesurfer mailing listFreesurfer(a)nmr.mgh.harvard.edu*MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://secure-web.cisco.com/1sA96g6MVXhTKqyIohE7iDpAeVudtNSoraQRr6PoymCFS6… <https://secure-web.cisco.com/1Aj-KIXWBSRBh4QYhiT5lPQzukbBDpNzMoSUI14TDJiN4-…> >>>>>> >>>>>> >>>>>> 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*MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* http://secure-web.cisco.com/1pcd3R17cw9CUmO-RFZqcKXMAKlR9Hi_f5yRd0WcMyKMI2V… <http://secure-web.cisco.com/1Kuqledw2eJViDlbH8MA0_r7jBLVXWD3VreLVXqKwRqHFX1…> . 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(a)nmr.mgh.harvard.edu*MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://secure-web.cisco.com/1sA96g6MVXhTKqyIohE7iDpAeVudtNSoraQRr6PoymCFS6… <https://secure-web.cisco.com/1Aj-KIXWBSRBh4QYhiT5lPQzukbBDpNzMoSUI14TDJiN4-…> >>>>>> >>>>>> >>>>>> 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*MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* http://secure-web.cisco.com/1pcd3R17cw9CUmO-RFZqcKXMAKlR9Hi_f5yRd0WcMyKMI2V… <http://secure-web.cisco.com/1Kuqledw2eJViDlbH8MA0_r7jBLVXWD3VreLVXqKwRqHFX1…> . 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(a)nmr.mgh.harvard.edu*MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://secure-web.cisco.com/1sA96g6MVXhTKqyIohE7iDpAeVudtNSoraQRr6PoymCFS6… <https://secure-web.cisco.com/1Aj-KIXWBSRBh4QYhiT5lPQzukbBDpNzMoSUI14TDJiN4-…> >>>>>> >>>>>> >>>>>> ___ >>>>>> Freesurfer mailing listFreesurfer(a)nmr.mgh.harvard.edu*MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://secure-web.cisco.com/1sA96g6MVXhTKqyIohE7iDpAeVudtNSoraQRr6PoymCFS6… <https://secure-web.cisco.com/1Aj-KIXWBSRBh4QYhiT5lPQzukbBDpNzMoSUI14TDJiN4-…> >>>>>> >>>>>> >>>>>> 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*MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* http://secure-web.cisco.com/1pcd3R17cw9CUmO-RFZqcKXMAKlR9Hi_f5yRd0WcMyKMI2V… <http://secure-web.cisco.com/1Kuqledw2eJViDlbH8MA0_r7jBLVXWD3VreLVXqKwRqHFX1…> . 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(a)nmr.mgh.harvard.edu*MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://secure-web.cisco.com/1sA96g6MVXhTKqyIohE7iDpAeVudtNSoraQRr6PoymCFS6… <https://secure-web.cisco.com/1Aj-KIXWBSRBh4QYhiT5lPQzukbBDpNzMoSUI14TDJiN4-…> >>>>>> >>>>>> >>>>>> 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*MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* http://secure-web.cisco.com/1pcd3R17cw9CUmO-RFZqcKXMAKlR9Hi_f5yRd0WcMyKMI2V… <http://secure-web.cisco.com/1Kuqledw2eJViDlbH8MA0_r7jBLVXWD3VreLVXqKwRqHFX1…> . 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 >>>>>> *MailScanner has detected a possible fraud attempt from >>>>>> "secure-web.cisco.com" claiming to be* >>>>>> https://secure-web.cisco.com/1sA96g6MVXhTKqyIohE7iDpAeVudtNSoraQRr6PoymCFS6… >>>>>> <https://secure-web.cisco.com/14NSCNEWI-E5xedPGXzQlT7gdo_k2vDQZC-njeqsKjvbqv…> >>>>> >>>>> >>>>> _______________________________________________ >>>>> Freesurfer mailing listFreesurfer(a)nmr.mgh.harvard.edu*MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://secure-web.cisco.com/1sA96g6MVXhTKqyIohE7iDpAeVudtNSoraQRr6PoymCFS6… <https://secure-web.cisco.com/1VZK27znP4ziWcnYrbJVNYOFT_9_5WAe5nVeyQOdMJhBJq…> >>>>> >>>>> >>>>> _______________________________________________ >>>>> Freesurfer mailing list >>>>> Freesurfer(a)nmr.mgh.harvard.edu >>>>> *MailScanner has detected a possible fraud attempt from >>>>> "secure-web.cisco.com" claiming to be* >>>>> https://secure-web.cisco.com/1sA96g6MVXhTKqyIohE7iDpAeVudtNSoraQRr6PoymCFS6… >>>>> <https://secure-web.cisco.com/1VZK27znP4ziWcnYrbJVNYOFT_9_5WAe5nVeyQOdMJhBJq…> >>>> >>>> >>>> _______________________________________________ >>>> Freesurfer mailing listFreesurfer(a)nmr.mgh.harvard.edu*MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://secure-web.cisco.com/1sA96g6MVXhTKqyIohE7iDpAeVudtNSoraQRr6PoymCFS6… <https://secure-web.cisco.com/1DOc6HK09tTHDCTRe3zaykFn4umMUwn8-y6MGj0gOXqv_Q…> >>>> >>>> >>>> _______________________________________________ >>>> Freesurfer mailing list >>>> Freesurfer(a)nmr.mgh.harvard.edu >>>> *MailScanner has detected a possible fraud attempt from >>>> "secure-web.cisco.com" claiming to be* >>>> https://secure-web.cisco.com/1sA96g6MVXhTKqyIohE7iDpAeVudtNSoraQRr6PoymCFS6… >>>> <https://secure-web.cisco.com/1DOc6HK09tTHDCTRe3zaykFn4umMUwn8-y6MGj0gOXqv_Q…> >>> >>> > _______________________________________________ > Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://secure-web.cisco.com/1sA96g6MVXhTKqyIohE7iDpAeVudtNSoraQRr6PoymCFS6…

1 0

Freesurfer Versions - Zeros in the Cortex
by Daniel Gutstein 06 Apr '21

06 Apr '21

External Email - Use Caution Hello, We are looking at the vertex-wise thickness measures for participants within the fsaverage space. There are a number of indices within the cortex that have thickness values of 0 in the thickness.fsaverage.mgh surface files. In FreeSurfer version 5.1, those same indices no longer have thickness 0 in the corresponding rh and lh fwhm smoothed thickness surface files due to the smoothing effect. However, in versions 6 and 7.1.1, the indices with 0 values remain 0 even in the fwhm smoothed files. Do you know why it was chosen that smoothing should have no impact on zeros in the later versions of FreeSurfer? Also, if we are interested in impacting the zeros from the later versions, is there a methodology which you would recommend? Thanks, Daniel

2 1

Problem with freesurfer measures
by Alberto Del Cerro Leon 06 Apr '21

06 Apr '21

External Email - Use Caution Hello Freesurfer team, I am using an annotation file that i've created previously to obtain the measures of some ROIs. To do that i am using de commands mri_surf2surf and mri_segstats. I want to obtain the following measures: 1. Gray and White Matter Volume 2. Folding Index 3. Curvature measures 4. Thickness However I don't know what surface in the surf folder of each subject I have to use. Could u help me?

3 11

unsubscribe
by Coleman, Katherine 06 Apr '21

06 Apr '21

Hello, Please remove me from the free surfer forum mailing list. Thank you, Katherine Katherine Coleman, MS Research Assistant II Mood Trajectories and Outcomes Laboratory Department of Psychiatry [cid:image001.jpg@01D6CE33.2A446E30]

1 0

Dicom Tag Problem Reconall
by Banu Femir 06 Apr '21

06 Apr '21

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

Re: [Freesurfer] recon-all bug
by zalewk 06 Apr '21

06 Apr '21

External Email - Use Caution Hi freesurfer team, I've tried running recon-all as mentioned before with the -xf flag under different conditions. As far as I can tell, any line using the UpdateNeeded function. e.g.: "set ud = `UpdateNeeded $thickness $pial $white`" fails with the following if statement because the variable $ud includes paths as strings in it instead of a 0/1 integer. Setting it to a 1 or 0 beforehand also seems to solve the problem. The function UpdateNeeded only seems to return an integer as an exit status, so I'm not sure why there are path strings in it causing it to fail. If I print out the $ud variable before it fails and the result is: "/subjectDirectory/subjectID_FREESURFER/mri mri mri_FREESURFER /subjectDirectory/subjectID_FREESURFER/mri/mri_FREESURFER/stats 1" It returns the exit status of 1 preceded by the path of the subject's mri directory, just "mri", "mri_FREESURFER" and the subject's stats directory (all subjects in this particular study have the suffix "_FREESURFER"). It prints this out these strings no matter the variables as .mgz file names, or number of variables passed to the UpdateNeeded function. I still don't have a clue what would cause this behavior. The UpdateNeeded function seems to work fine and as intended as far as I can tell, so I still don't know why these paths/strings are being added and causing it to crash. Best, Kody Zalewski Message: 3 Date: Fri, 02 Apr 2021 03:49:02 +0200 From: fsbuild <fsbuild(a)contbay.com> Subject: Re: [Freesurfer] recon-all bug To: freesurfer(a)nmr.mgh.harvard.edu Cc: cmacd(a)neurosurgery.washington.edu Message-ID: <1617328142.6066780ef2824(a)trashmail.com> Content-Type: text/plain; charset="utf-8" External Email - Use Caution Hello Kody, One thing you could try to get more information printed about what is going on is to edit the very first line in the recon-all script to be: #! /bin/tcsh -xf ? instead of #! /bin/tcsh -f Adding the x option will echo each line in the script as it?s run with the variable values expanded, and seeing that output could help with debugging. - R. On Apr 1, 2021, at 20:29, zalewk <zalewk(a)uw.edu> 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 fo r 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, Kody Zalewski_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer?

2 1

recon-all bug
by zalewk 06 Apr '21

06 Apr '21

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, Kody Zalewski

2 1

retaining label ids
by miracle ozzoude 06 Apr '21

06 Apr '21

External Email - Use Caution Hello Experts, I did like to extract wm whilst retaining the label ids. I tried mri_extract_labels but it didn't work. Any help would be appreciated. Many thanks, Paul

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 April 2021