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30131 discussions

Thalamic segmentation error Big Sur
by Daniela Vecchio 16 Jul '21

16 Jul '21

External Email - Use Caution Hello FreeSurfer Developers, I'm attempting to segment thalamic nuclei, as described by the tutorial page (https://secure-web.cisco.com/1F9Cs4OMcQ2PV75K6Q0sKfyHoo5UBJNkIWoWVANuievmgb…) but I got an Matlab routine error. I’t happened after the upgrade to MacOS Big Sur and I guess it is a compatibility issue. I tried also to re-install the routine (by fs_install_mcr R2014b ) and to run the process by docker container but the process ended with the same error. (Obviously, I got the same error also trying the hippocampus&amygdala module). ERROR: MATLAB is exiting because of fatal error /Applications/freesurfer/bin/run_SegmentThalamicNuclei.sh: line 33: 3322 Killed: 9 /Applications/freesurfer/bin/SegmentThalamicNuclei.app/Contents/MacOS/SegmentThalamicNuclei subjHC001/ /Applications/freesurfer/subjects 0.5 /Applications/freesurfer/average/ThalamicNuclei/atlas/AtlasMesh.gz /Applications/freesurfer/average/ThalamicNuclei/atlas/AtlasDump.mgz /Applications/freesurfer/average/ThalamicNuclei/atlas/compressionLookupTable.txt 0.05 L-BFGS v12 '/Applications/freesurfer/bin/fs_run_from_mcr /Applications/freesurfer/bin/' 1 0 Darwin iMac-di-Daniela.local 20.5.0 Darwin Kernel Version 20.5.0: Sat May 8 05:10:33 PDT 2021; root:xnu-7195.121.3~9/RELEASE_X86_64 x86_64 I've searched the list and I didn’t found a way to fix it. Does anyone have any thoughts on how to trouble-shoot this one? Also, Ive attached the thalamic-nuclei-mainFreeSurferT1.log in case it's of any use. Thanks in advance Best regards, Daniela

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/usr/pubsw reference in 7.1.1
by Drucker, Daniel 16 Jul '21

16 Jul '21

When running tksurfer in 7.1.1 (from https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/7.1.1/freesurfer-lin… ) , I get: Tcl_Init failed: Can't find a usable init.tcl in the following directories: /usr/pubsw/packages/tcltktixblt/current/lib/tcl8.4 This probably means that Tcl wasn't installed properly. Tk_Init failed: invalid command name "tcl_findLibrary" Tix_Init failed: Can't find a usable Tix Init.tcl in the following directories: ./library ./tix8.1 ./library ./tix8.1 /usr/pubsw/packages/tcltktixblt/current/lib/tix8.1 This probably means that Tix wasn't installed properly. What should I do about this? It works under 6.0.1. -- Daniel M. Drucker, Ph.D. Director of IT McLean Hospital Imaging Center Harvard Medical School

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Follow-up: PVC to calculate myelin maps
by Thalhammer, Melissa 16 Jul '21

16 Jul '21

External Email - Use Caution Dear FS-experts, I want to create myelin maps out of T1w/T2w contrasts and I have already read this e-mail conversation from the archive: <https://secure-web.cisco.com/1ys6IhakVz9GhQ8cHqjngCPDL_6cj2C64AxUoa21H6uDav…> https://secure-web.cisco.com/1ys6IhakVz9GhQ8cHqjngCPDL_6cj2C64AxUoa21H6uDav…. It is suggested to use the PVC function of PETsurfer on the T1/T2 ratio. However, I have trouble understanding which commands are necessary for this task. How is the T1/T2 ratio obtained? Did I understand correctly that then running gtmseg and mri_gtmpvc described in https://secure-web.cisco.com/1GCM3hPGgpuFPwg4AB7NHiJDqWsdiXhsPTtVOqPiJrwuVi… are sufficient or are additional functions necessary? For mri_gtmpvc, what flags are required (since usually --i defines a PET image which we of course don't have)? Best, Melissa Thalhammer

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FIR analysis and task regressor (continued) & slice-timing correction
by Doll, Laura 16 Jul '21

16 Jul '21

External Email - Use Caution Hi, Back in February I already had some issues with FIR analysis using a task regressor. In the meantime, I switched to other analysis. But now we would want to try that again. I attached the old mails below, but since the problem slightly changed, I'll describe them again: I want to run an analysis with the normalized pupil size as task regressor. Because the pupil dilation response itself is already slow (peaking after ~1s), we thought it would be good to use FIR instead of assuming a certain shape of HRF. I tried two different analysis: 1) mkanalysis-sess -fsd bold -stc siemens -surface fsaverage lh -fwhm 5 -notask -fir 2 15 -TR 2 -polyfit 2 -analysis PupP_fir.lh -per-run -taskreg PupPAvg 1 2) same with "-event-related -nc 2 -paradigm paradigm.txt" instead of -notask. With 1), the analysis does run without errors but I don't get to see a time course when plotting with tksurfer-sess and I don't know what exactly is plotted than (the maximum or the first time point or...?). With 2) I arrive at a similar point as in February: when I try to plot the results, I get this error: ERROR: could not determine file for ./S05/bold/PupP_firTask.lh/h The h.nii.gz file is indeed not there. If I copy h-offset.nii.gz and rename the copy to h.nii.gz, tksurfer-sess opens including the time course viewer. But this shows does not show a time course. So the question is: How do I get time courses for this FIR analysis with a task regressor? Where is my mistake? And a slightly off-topic question regarding task regressors & slice timing: As far as I know, stc shifts all slices to TR/2 and with the default stimulus delay parameter, TR/2 is also added to the times in paradigm files. But how does it work for task regressors? Do I have to give "corrected" values? I.e. in my case I average the pupil size over TR in order to arrive at the desired number of time points. But should I do that around the original start of the sequence or around the "corrected" time (i.e. +TR/2)? Many thanks in advance, Laura On 2/5/2021 2:08 AM, Doll, Laura wrote: External Email - Use Caution Hi Doug, Thanks for your response. No, I did not demean the task regressor... do I have to? Yea, probably a good idea Exactly. When I try to run tksurfer-sess, it complains about the missing file "h". When I rename the "h-offset" file to "h", I can run tksurfer-sess and I do see a map. The time course viewer opens as well but it only shows one time point. Not sure here (have not run FIR in a long time). I noticed that you have -notask on your mkanalysis command. Have you tried it without -notask? I can also continue to run the group analysis. During "isxconcat-sess" it while again complain about the missing file but mri_glmfit and following commands still work. So I do get a group map but I am not sure what it shows. Depends on the contrast, but I think it should create maps for each time point in the FIR window. Best, Laura Did you demean the task regressor? Is the problem that you cannot run tksurfer-sess? Or are you reporting multiple problems? On 2/3/2021 8:32 AM, Doll, Laura wrote: External Email - Use Caution Hi everyone, Is it possible to do an FIR analysis using a task regressor instead of (or additional to) a paradigm file? More precisely, we want to use pupil size as task regressor. It was recorded during an auditory detection task (event related). This works when I use "-spmhrf" or other HRF options. However, for FIR I cannot get the expected time course in the single subjects data. Tksurfer ends with an error because it cannot find the file h.nii.gz: ERROR: could not determine file for [...]/S01_3/bold/PupilFIR.lh/h This file indeed does not exist, there is only one called "h-offset". The commands I used until that point are (here neglecting the original task, but using -event-related etc instead of no task results in the same error): mkanalysis-sess -fsd bold -stc up -surface fsaverage lh -fwhm 5 -notask -fir 4 20 -TR 2 -polyfit 2 -analysis PupilFIR.lh -per-run -taskreg Pupil 1 selxavg3-sess -s S01_3 -analysis PupilFIR.lh tksurfer-sess -s S01_3 -analysis PupilFIR.lh -call -tksurfer Is there any solution for this? Or any reason why it should not be done that way? Best, Laura _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://secure-web.cisco.com/1n9wxgcJ7Tc0qfJejA8xVei3ZUL3PGBbuAJFZvOdieNEW7… _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://secure-web.cisco.com/1n9wxgcJ7Tc0qfJejA8xVei3ZUL3PGBbuAJFZvOdieNEW7…

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Qdec vertex-wise clustering question
by Alejandro Meruelo 15 Jul '21

15 Jul '21

External Email - Use Caution Hello, I had a brief question regarding Qdec vertex-wise clustering. Does Qdec use the data in the raw imaging files or the qdec.tables.dat file to generate the vertex-wise clustering results for cortical thickness group comparisons? Many thanks for your assistance, Alejandro

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question about longitudinal data analyses
by Ritobrato Datta 15 Jul '21

15 Jul '21

External Email - Use Caution Hi All, I have the following data – I have 205 subjects - each subject was imaged at 3 timepoints (baseline, followup 1 and followup 2) The 205 subjects are split in two treatment arms with 100 subjects in the first one and 105 subjects in the second one. For each timepoint, I have created FA maps in their native diffusion space. I have also extracted the mean FA maps for 187 ROIs using mri_segstats. For each timepoint, I have saved the results as a matrix (FA in 187 ROIs x 205 subjects) in a text file. So I have three files for the three timepoints. I have the age and cognitive score for each subject at each timepoint. And their gender. I want to answer the following questions – 1. Do the baseline FA correlate with the corresponding cognitive score at baseline ? 2. I am interested in testing whether the FA changed significantly across the different timepoints and does that relate to the change in the cognitive score 3. Is there an effect of treatment on this change in FA across time ? Can you please suggest what programs in freesurfer will allow me to test these questions on both voxelwise and ROI wise ? Many thanks for your help and guidance, Regards Rito

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Re: [Freesurfer] Freesurfer Digest, Vol 209, Issue 11
by Thalhammer, Melissa 15 Jul '21

15 Jul '21

External Email - Use Caution Dear Mr. Greve, does gamma.table.dat contain the corrected residuals then? or z-scored values? Best, Melissa ________________________________ Von: freesurfer-bounces(a)nmr.mgh.harvard.edu <freesurfer-bounces(a)nmr.mgh.harvard.edu> im Auftrag von freesurfer-request(a)nmr.mgh.harvard.edu <freesurfer-request(a)nmr.mgh.harvard.edu> Gesendet: Samstag, 10. Juli 2021 18:00:02 An: freesurfer(a)nmr.mgh.harvard.edu Betreff: Freesurfer Digest, Vol 209, Issue 11 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/1FW61lXn8l78S0vQ7bKMcbs-HzVt_ZpYs4pbpEzUdSVZrY… 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. Re: Cortical thicknees normalization values (Douglas N. Greve) 2. Re: Calculating group-wise Dice Similarity Coefficient and corresponding surface map (Douglas N. Greve) 3. Re: smoothing volume data extracted using aparcstats2table (Douglas N. Greve) 4. Hippocampal Subfield Definition Errors (Franchesca Kuhney) 5. Re: Problem with mri_glmfit-sim (Douglas N. Greve) 6. Re: recon-all soft errors (Douglas N. Greve) 7. Re: mri_glmfit DOSS (Douglas N. Greve) 8. Re: LGI FS 7.1 (Douglas N. Greve) 9. Re: Can I extract GLM values? (Douglas N. Greve) 10. Re: fcseed-config (Douglas N. Greve) 11. Re: Help segmenting all subjects in a folder (Douglas N. Greve) 12. Re: Question about Extracting QDEC Results (Douglas N. Greve) 13. Re: Edit pial surface (Douglas N. Greve) 14. Re: Hippocampal Subfield Definition Errors (Iglesias Gonzalez, Juan E.) 15. Re: What is the relationship between qdec results and aparc.stats? (Douglas N. Greve) 16. Re: setwdelay error 1 weight (Douglas N. Greve) 17. Re: Transformation Applied to T1.mgz during recon-all (Douglas N. Greve) 18. Re: Visualizing specific cortical parcels in Desikan Killiany atlas (Douglas N. Greve) 19. Re: Freesurfer longitudinal stream error (Douglas N. Greve) 20. Re: LGI FS 7.1 (Del Re, Elisabetta) 21. Re: question about longitudinal data analyses (Douglas N. Greve) 22. Average intensity from functional image within a label along the surface (Erik Jahner) ---------------------------------------------------------------------- Message: 1 Date: Fri, 9 Jul 2021 12:40:13 -0400 From: "Douglas N. Greve" <dgreve(a)mgh.harvard.edu> Subject: Re: [Freesurfer] Cortical thicknees normalization values To: freesurfer(a)nmr.mgh.harvard.edu Message-ID: <f3f7c9b2-9e2d-80c3-4d5e-c4c92359d4e1(a)mgh.harvard.edu> Content-Type: text/plain; charset="windows-1252" We generally do not normalize it by anything. ICV norm is not needed because thickness does not scale with head size. Sometimes people will normalize by mean thickness, but that changes the question being answered, so that is more a question for you On 6/24/2021 3:01 PM, Gabbo Ram?rez Garc?a wrote: > > ????????External Email - Use Caution > > ????????External Email - Use Caution > > > > Hi freesurfer user. > > I have been working with some cortical thickness values of a control > group to test some changes related to cognitive training. However, I > have been hesitating about whether I have to normalize the cortical > thickness values (as happens with subcortical volumes and ICV) or not. > I have read a little about it and I understood that I could use the > ICV or/and mean cortical thickness, but I didn't find a specific > criteria to do or not this normalization. Any clue, recommendation, > explanation or paper about this will be very helpful. > > Thanks in advance. > > *or reposting?discussion?of this question. > > *Gabriel R.* > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://secure-web.cisco.com/1igRZreQyL28dpaDxcw1KUE3935aWbqlbZ8jIEL5JY7Fol…

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mcprextreg file structure and X
by Erik Jahner 15 Jul '21

15 Jul '21

External Email - Use Caution Dear all, I am trying to figure out the structure of X.dat and where the mcprextreg parameters are in the table. It is my understanding that the mcprextreg is the resulting PCA on the motion to generate a nuisance variable for motion. I see the following regressors clearly: my ROI, global regressor, PCA-wm, and PCA-csf. There are however, additional columns none of which line up with the mcprextreg file for that participant. Can someone explain how the mcprextreg file gets processed and entered into the X.dat file with it is used as a nuisance regressor? I have also checked the fmcpr.mcdat but I also cannot find this in the X.dat data set ~Erik Jahner

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how to visualize statistical maps in FS7.1?
by Bernardoni, Fabio 15 Jul '21

15 Jul '21

External Email - Use Caution Dear Freesurfers I recently moved to FS7.1 and I was trying to reproduce my workflow I had with FS5.3. To visualize statistical maps, I had always used tksurfer. It seems, however, it is no longer maintained. When I launch it it fails to find out the tix, tcl, etc libraries. Following this thread: https://secure-web.cisco.com/1v7sQGKZgCQ9d6BT0fUpIf9QvmP5selhkoGYWs1-X9TSsF… I tried to use tksurferfv. However, when trying to overlay the sig.mgh output of mriglmfit, on an inflated fsaverage surface, the program shuts down, with this error: freeview -f /usr/local/freesurfer/subjects/fsaverage/surf/lh.inflated:curvature=/usr/local/freesurfer/subjects/fsaverage/surf/lh.curv -viewport 3d terminate called after throwing an instance of 'int' Abort (core dumped) What would you suggest to visualize statistical maps in FS7? Is my problem expected? Thank you in advance for your attention Fabio Dr. Fabio Bernardoni wiss. Mitarbeiter Division of Psychological & Social Medicine and Developmental Neurosciences http://secure-web.cisco.com/1fJ-kcGEyM5xIf9EYKEBdxq9jOYgp4LWrcrsRqW2VW0t2Xh…; http://secure-web.cisco.com/1xug_1JvXuCXLAVwiFYmOgWpcXQT14Ee7lkNin2N9gXlkJe… +49 (0351) 458-5245 Universitätsklinikum Carl Gustav Carus an der Technischen Universität Dresden Anstalt des öffentlichen Rechts des Freistaates Sachsen Fetscherstraße 74, 01307 Dresden http://secure-web.cisco.com/1ymiT7HwdvqBcrZ2JgPJohlSR2r6RJdo68pLuJ1xGc6Cx6E… Vorstand: Prof. Dr. med. D. M. Albrecht (Sprecher), Katrin Erk Vorsitzender des Aufsichtsrates: Prof. Dr. G. Brunner USt.-IDNr.: DE 140 135 217, St.-Nr.: 203 145 03113 http://secure-web.cisco.com/1ymiT7HwdvqBcrZ2JgPJohlSR2r6RJdo68pLuJ1xGc6Cx6E… Vorstand: Prof. Dr. med. D. M. Albrecht (Sprecher), Wilfried E. B. Winzer Vorsitzender des Aufsichtsrates: Prof. Dr. G. Brunner USt.-IDNr.: DE 140 135 217, St.-Nr.: 203 145 03113

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Freesurfer not creating specific files
by Taylor, Lisa Marie 15 Jul '21

15 Jul '21

External Email - Use Caution Hi everyone, I could really use some help with figuring out an issue I've been struggling with the last few months. It seems that when I run recon-all on over 20 of my participants, not all freesurfer files are created. But I am not understanding why, and my technical capabilities are limited. Particularly, it seems there's an issue reading the lh.BA1_exvivo.label. I will attach the recon-all log file for any other information that it can provide. Also, I run a script for recon-all and these are the arguments: srun ${FREESURFER_HOME}/bin/recon-all -s imagedir/subid -no-isrunning -all -hippocampal-subfields-T1 -brainstem-structures -qcache Not sure if this is pertinent, but our HPC has been updated, but I am unaware if that can impact how freesurfer is run. Thank you for any insight you can provide! Lisa (I previously sent an email with screen shots, but the email was waiting to be approved due to size) ________________________________ This message may contain confidential information and is for the sole use of the intended recipient(s). If you are not the intended recipient, do not use, distribute, or copy this e-mail. Please notify the UC Irvine Health – Compliance and Privacy Office via email at hacompliance(a)uci.edu or by phone 888-456-7006 immediately if you have received this e-mail in error. E-mail transmission cannot be guaranteed to be secure or error-free as information could be intercepted, corrupted, lost, destroyed, arrive late or incomplete, or contain viruses. The sender therefore does not accept liability for any errors or omissions in the contents of this message, which arise as a result of e-mail transmission.

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