Freesurfer May 2020

freesurfer@nmr.mgh.harvard.edu

111 participants
208 discussions

Feat to fsfast
by Alshelh, Zeynab 27 May '20

27 May '20

Hi all, Is it possible to do the first level unsmoothed using feat and the second level surface based group analysis using fsfast? Thanks, ---- Zeynab Alshelh, PhD | Postdoctoral Research Fellow Pain and Neuroinflammation Imaging Laboratory Harvard Medical School | A. A. Martinos Center for Biomedical Imaging Massachusetts General Hospital | 149 Thirteenth Street, Room 1101 Charlestown, MA 02129 +1 (617) 794 6838 zalshelh(a)mgh.harvard.edu | www.nmr.mgh.harvard.edu

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Are my slice-time corrected files being used in selxavg3-sess?
by Mcnorgan, Christopher 27 May '20

27 May '20

External Email - Use Caution Hi all, There was some ambiguity in communication from a previous MR technician regarding the slice ordering in our BOLD data. preproc-sess was applied to our data: preproc-sess -sf SUBJECTS -surface fsaverage lhrh -per-run -fsd bold -sliceorder up -fwhm 4 I then ran selxavg3-sess on the data, followed by mri_glmfit to produce contrast maps As an experiment, I deleted the fmcpr.up.* data, and re-ran preproc-sess, this time specifying sliceorder down: preproc-sess -sf SUBJECTS -surface fsaverage lhrh -per-run -fsd bold -sliceorder down -fwhm 4 After re-running selxavg3-sess and mri_glmfit on the reverse-stc-corrected data, the contrast maps were identical, which seemed peculiar, given that the slice time corrections for a 2-second TR were in the opposite direction. I note that when I run selxavg3-sess, it generates a set of fmcpr.sm4 files, and I suspect that the GLM is run on those novel non-stc files. Is there a switch I am missing in the call to selxavg3-sess or mkanalysis-sess that will ensure that will allow me to ensure that the GLM is run on fmcpr.[STC].sm4.fsaverage.[rl]h.nii.gz? Thanks /********************************************** * Chris McNorgan * Assistant Professor * Department of Psychology * University at Buffalo, * The State University of New York * http://ccnlab.buffalo.edu/ * Office: 716.645.0236 * Lab: 716.645.0222 **********************************************/

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Command cannot recognise session from sessid file
by Marco Ninghetto 27 May '20

27 May '20

External Email - Use Caution Dear experts, I looked through your mailing list, but I cannot find any question like mine. When I run whatever command in my analysis for retinotopy, I have to specify subject after subject using: -s subj001 -s subj002 -s subj00x and so on. To avoid that, inside my project directory, I have the "sessid" (actually two sessid files) file in which are listed all the names of the subjects. I don't know why, when I try to run: -sf sessid1 I get the error, like (random command from my pipeline): brain@neurodebian:/media/main/fs_pRFs_functionals$ isxconcat-sess -sf sessid1 -a rtopy.fsaverage.lh/ -call -o retgroup_ng ERROR: finding sessions ERROR: cound not find session SUBJ02NG I tried to write differently inside the sessid file, I tried to use the name of the structural folders instead of the functional ones, but nothing seems to work. My sessid file is something like this: SUBJ02NG SUBJ06NG SUBJ07NG SUBJ08NG and so on.Each subject's session folder name: SUBJ02NG SUBJ06NG SUBJ07NG SUBJ08NG The names listed are the same for the name of the session folder for each subject, but still, FS tells me that it cannot find the session. [image: tree.png] Inside each subject folder, there is the "bold" folder and inside that, together with the runs folders, there is the analysis folder. Any idea on what I'm doing wrong? Thank you so much, Marco -- --------------------------------------------------- Marco Ninghetto, PhD candidate Laboratory of Neuroplasticity Nencki Institute of Experimental Biology Polish Academy of Sciences 3 Pasteur Street, 02-093 Warsaw, Poland

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ERROR: mri_fill: could not find any points where lh and rh wm are nbrs
by Marina Fernández 27 May '20

27 May '20

External Email - Use Caution Dear Freesurfer experts, When I run "recon-all -autorecon2-wm -subjid post_006" I get the following error: ... #-------------------------------------------- #@# Fill Tue May 26 16:13:33 CEST 2020 /usr/local/freesurfer/subjects/post_006/mri mri_fill -a ../scripts/ponscc.cut.log -xform transforms/talairach.lta -segmentation aseg.auto_noCCseg.mgz wm.mgz filled.mgz logging cutting plane coordinates to ../scripts/ponscc.cut.log... INFO: Using transforms/talairach.lta and its offset for Talairach volume ... using segmentation aseg.auto_noCCseg.mgz... reading input volume...done. searching for cutting planes...voxel to talairach voxel transform 1.03994 0.01456 0.07738 -16.87541; -0.02607 1.18971 0.24142 -16.40842; -0.06544 -0.23822 1.03825 18.09422; 0.00000 0.00000 0.00000 1.00000; reading colortable from MGH file... colortable with 14176 entries read (originally /usr/local/freesurfer/FreeSurferColorLUT.txt) voxel to talairach voxel transform 1.03994 0.01456 0.07738 -16.87541; -0.02607 1.18971 0.24142 -16.40842; -0.06544 -0.23822 1.03825 18.09422; 0.00000 0.00000 0.00000 1.00000; reading segmented volume aseg.auto_noCCseg.mgz... mri_fill: could not find any points where lh and rh wm are nbrs No such file or directory Linux sleep2014 4.13.0-45-generic #50~16.04.1-Ubuntu SMP Wed May 30 11:18:27 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux recon-all -s post_006 exited with ERRORS at Tue May 26 16:13:41 CEST 2020 To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting I have seen in other questions that this error may be due to the CC and the aseg files, and it is interesting because when I load aseg.auto.mgz or aseg.auto_noCCseg.mgz files in Freeview, the following message in Freeview terminal is shown in red: "colortable with 14176 entries read (originally /usr/local/freesurfer/FreesurferColorLUT.txt)", when I think they should be 1475 entries. I'm using freesurfer v6.0. Could you help me to solve this problem? Thank you in advance! Marina.

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the -label flag in mri_cnr
by Pradyumna Bharadwaj 27 May '20

27 May '20

External Email - Use Caution Hello! I had a couple of questions about how mri_cnr computes the contrast to noise ratio. From previous posts, a command such as mri_cnr $FREESURFER_HOME/subjects/bert/surf $FREESURFER_HOME/subjects/bert/mri/norm.mgz gives the lh cnr, rh cnr, and total cnr for bert. 1) What exactly is happening when you reference the /surf directory here? 2) Are the CNR values for the norm.mgz volume being computed by using the lh white + lh pial; and rh white + rh pial surfaces? 3) Are the subcortical gm structures somehow involved in this calculation as well? I'm asking question 3 because when you add a -label $FREESURFER_HOME/subjects/bert /label/lh.cortex.label $FREESURFER_HOME/subjects/bert/label/rh.cortex.label the lh cnr, rh cnr, and total cnr values that you get are now different. The outputs for bert for each case is as follows (FreeSurfer v6 bert was used here): 1) *With /surf alone* white = 96.6+-6.0, gray = 75.7+-13.5, csf = 55.3+-16.6 gray/white CNR = 1.983, gray/csf CNR = 0.907 *lh CNR = 1.445* white = 96.4+-6.0, gray = 76.0+-13.3, csf = 55.6+-16.2 gray/white CNR = 1.952, gray/csf CNR = 0.943 *rh CNR = 1.448* *total CNR = 1.446* *2) With /surf and -label * white = 96.6+-6.0, gray = 73.1+-18.9, csf = 50.8+-20.5 gray/white CNR = 1.389, gray/csf CNR = 0.644 *lh CNR = 1.016* white = 96.4+-6.0, gray = 73.4+-18.8, csf = 51.0+-20.3 gray/white CNR = 1.353, gray/csf CNR = 0.652 *rh CNR = 1.002* *total CNR = 1.009* Any inputs or thoughts on this matter are greatly appreciated! Thanks, Prad

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Thalamic Segmentation of Post Contrast MRI
by barış genç 26 May '20

26 May '20

External Email - Use Caution Dear FreeSurfer Experts, I have a data set (control and patients) that has 3DT1 , acquired on 3 T Philips Achieva scanner after post contract (Gadolinium). Can I use his data set to measure the thalamic nuclei segmentation or amygdala segmentation? Is gadolinium can interferes results? Any suggestions will be great.

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BIDS Derivatives final request for comments
by Franklin Feingold 25 May '20

25 May '20

External Email - Use Caution The BIDS community is preparing to merge the Common Derivatives extension. The updated draft is available for review at https://bids-specification.readthedocs.io/en/common-derivatives/, and comments and suggestions may be submitted on GitHub at https://github.com/bids-standard/bids-specification/pull/265. The scope of this extension is establishing a set of common principles for organizing derivative datasets, dataset-level metadata, and naming conventions for minimally preprocessed files. Additionally, some common imaging derivatives (e.g., brain masks) have been specified. More detailed modality-specific derivatives are scheduled for inclusion in the next few months. The final review process entails a minimum of one week for public comment, with a possibility of extension for unresolved discussion. Once public comments are concluded, there will be a one week freeze, during which only critical issues will be considered. (For more details on the release protocol, see https://github.com/bids-standard/bids-specification/blob/master/Release_Pro….) We look forward to hearing your feedback! Franklin

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Re: [Freesurfer] Display Errors in Freeview
by fsbuild 25 May '20

25 May '20

External Email - Use Caution Hello Nils, The first thing to check would be the video memory - I would try to give it the maximum. Another thing to check if that does not help is the CPU's.  You could try increasing it from say 1 to 2 CPU's if you have a 4 core machine. Take a look at the instructions we post for setting up a VM (and we also have an Ubuntu VM to download with FS 6 and 7 on it) - see,https://surfer.nmr.mgh.harvard.edu/fswiki/VM_67 -R. On May 23, 2020, at 14:16, Nils Böer <nils.tobias94(a)gmail.com> wrote:        External Email - Use Caution        Hello everyone,I'm new to Freesurfer and just got started. I have to analyze data which is already prepared (recon-all is already done). I can load my subjects data into freeview but when i start working on it, e.g. clicking through the slices my freeview (6.0) just freezes everytime without an error message. I can use the mouse to click or scroll through with the arrows but nothing happens on the screen anymore. Sometimes the display in freeview also starts to get gray and i can't see anything of the mri scan anymore (examples are in appendix).I'm running freesurfer 6.0.0 on a Win10 Computer with the Oracle VirtualBox using Ubuntu 18.04.4 LTS. I hope you can help me, i couldn't find anything related to this problem. Can it be related to problems with the RAM (Virtualbox is allowed to use 10GB of Ram).?Best regards,Nils-- Nils BöerResearch Assistant with Bachelor Degree (WHB) Psychology and MovementUniversity of PaderbornDepartment of Sports and HealthWarburger Str. 10033098 PaderbornRoom: Sp 1.401Email: nils.tobias94@gmail.com / nboeer@mail.uni-paderborn.deWeb: https://sug.uni-paderborn.de/en/sport/sportpsychologie/team/         https://sug.uni-paderborn.de/department/it/Virenfrei. www.avast.com<Freeview display error and frozen.png>_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Re: [Freesurfer] circular/cyclic color map for polar data in freeview
by Devavrat Vartak 24 May '20

24 May '20

External Email - Use Caution Hi, Yes, it remains linear i.e it does not warp around. I am trying to display my theta (polar) values, and a circular map will help. Additionally, I am trying to determine why my distribution of data (in freeview) seems different compared to when I just plot my theta(polar) as a histogram. Thank you! (Apologies, if this reply doesn't reach the intended thread) Cheers, DV On Tue, May 19, 2020 at 7:27 PM <freesurfer-request(a)nmr.mgh.harvard.edu> wrote: > Send Freesurfer mailing list submissions to > freesurfer(a)nmr.mgh.harvard.edu > > To subscribe or unsubscribe via the World Wide Web, visit > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > 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. Freeview on debian (Gian Marco Duma) > 2. Uploading fs7.1 to hms o2 cluster > (Zeng, Victor (BIDMC - Keshavan - Psychiatry)) > 3. Re: Volume timeseries to native and fsaverage (?zen? ta?k?n) > 4. Re: FREESURFER-7.1: recon-all exited with error "ERROR: > cannot find or read transforms/talairach.m3z" (Safi Ullah .) > 5. circular/cyclic color map for polar data in freeview > (Devavrat Vartak PhD) > 6. Re: Freeview on debian (fsbuild) > 7. Re: Freesurfer Digest, Vol 195, Issue 47 (Douglas N. Greve) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Tue, 19 May 2020 18:14:38 +0200 > From: Gian Marco Duma <gianmarco.duma(a)phd.unipd.it> > Subject: [Freesurfer] Freeview on debian > To: freesurfer(a)nmr.mgh.harvard.edu > Message-ID: > <CABaZGscZTrMVq2AVhahXuXgwiHKgwTfrPe= > ywxLiqitz_3+qhg(a)mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > External Email - Use Caution > > Hi everyone, I have a problem with freeview. My university created for me a > virtual machine in a small analysis cluster. Unfortunately, they installed > Debian 4.19.98. I read that freeview has some problems with Debian, and in > fact I am not able to open it. Unfortunately I need to visualize the data > because we are conducting an anatomical study with patients with lesions. > All the processes I ran until now, like automatic segmentation and surface > generation like recon all, worked perfectly, but I need to visualize the > data. Do you have suggestions to solve this problem? > Thanks >

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FSFAST retinotopy output interpretation: questions {Disarmed}
by Kasia Siuda-Krzywicka 24 May '20

24 May '20

External Email - Use Caution Dear FreeSurfer community, I am running retinotopy analysis with FSFAST using: - FreeSurfer version: FSBUILD freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c - on Linux 4.15.0-55-generic I have only the polar angle condition, in two runs, one with positive and second with negative direction. To process the data, I followed the steps listed here: https://kylemathewson.com/retinotopy-in-freesurfercnl-protocol/#FUNC For the analysis to run, I created "dummy" eccentricity folders, as advised here: https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg48640.html The pipeline seem to have worked (no error messages, no warnings, I enclose the analysis.info <http://mkanalysis.info/> and the selxavg.log files). I am now trying to visualize the data to check the results. In the tutorial I followed, it is recommended to view the real.nii.gz and imag.nii.gz files. You will find the screen shots of those files visualized in freeview attached. To my eyes, none of those images look like polar angle retinotopy maps. I then visualized the angle.masked file (if I understand correctly, it is the angle map masked with p=0.01 significance), you can find the screen shot attached. It also doesn't look right, more importantly - it doesn't seem to be masked by significance. I have then followed the visualization instructions from the official FreeSurfer wiki, i.e: tksurfer-sess -a rtopy.self.?h -s sessid -map angle.masked I attach the screen shot (tk_surfer_file.png). Frankly, I'm not sure what I'm looking at there :) Looking for documentation that would describe retinotopy output files, I found the selfreq.pdf file, a documentation explaining *programs for computing the amplitude and phase of the hemodynamic response at a certain frequency.* In this file I found a c shell script to visualize the processed data: #!/bin/csh -f set name = subject # put the subject’s name here set hemi = lh setenv eccendir eccen setenv polardir polar 4 #setenv patch occip.patch.flat setenv revpolarflag 1 setenv rgbname eccenthinmot setenv fthresh 0.4 setenv fslope 1.3 setenv fmid 0.8 setenv angle_offset 0.77 setenv noexit tksurfer -$name $hemi I adjusted this script to my environment and run it on my machine. It doesn't work because it's missing the following input files: sigf-lh.w sig2-lh.w sig3-lh.w Indeed, those files do not exist in my folders. Does it mean that I made a mistake somewhere in the pipeline? Should those files be in my folders? To sum up, these are my questions: 1) Do the enclosed maps seem alright to you? 2) If not, do you have any idea at which processing stage there was an error? Or is it just a visualisation issue? 3) If this is a visualization error, how should I visualize the angle maps in freeview? Specifically, what output files should I use for this visualization? More specifically, what commands should I use to visualize these output files? For your information, these are my output files in the retino.lh/polar folder: angle.masked.nii.gz cesvar.nii.gz fsig.nii.gz mc.sig.dat angle.nii.gz cesvarpct.nii.gz imag.nii.gz minsig.nii.gz cesmag.nii.gz cwmap-imag.nii.gz iminsig.nii.gz real.nii.gz cesmagpct.nii.gz cwmap-real.nii.gz mag.nii.gz sig.nii.gz ces.nii.gz efficiency.dat mc.ces.dat z.nii.gz cespct.nii.gz F.nii.gz mc.minsig.dat 4) what do the imag.nii and real.nii maps correspond to? I believe they represent the real and imaginary component of the Fourier transform, but how do I interpret it in terms of retinotopy results? I would be very grateful for any help. Take care, Kasia -- Kasia Siuda-Krzywicka, PhD Physiological Investigation of Clinically Normal and Impaired Cognition Lab Institut du Cerveau et de la Moelle Épinière 47 bd. de l’Hôpital 75013 Paris office: +33 (0)1 57 27 41 53 mobile: +33 (0)6 52 69 46 49

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Freesurfer May 2020