Freesurfer

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30084 discussions

Citation of hard and soft failures
by Monereo Sanchez, Jennifer (RAD) 27 May '20

27 May '20

External Email - Use Caution Dear all, I am writing a paper for which I need to introduce the concepts of "hard" and "soft failures", and I am wondering what is the proper way of citing them. I am aware there is plenty of material online (see for example https://fscph.nru.dk/slides/Allison/freesurfer.failure_modes.pdf) but I am wondering if there is a citable paper in which these are described or discussed. Best wishes, ?Jennifer Monereo

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recon-all misses part of occipital cortex
by Isaac Adanyeguh 27 May '20

27 May '20

External Email - Use Caution Dear Freesurfer Development Team, I am having some issues with recon-all where it misses a huge chunk of the occipital cortex in several of my subjects. I have searched the archive and have not found any report of similar issues. Could you please help me figure out how to solve this issue. I have attached a screenshot showing the missing occipital cortex segmentation and a copy of the recon-all.log. I performed the analysis using: - Freesurfer version: freesurfer-Linux-centos6_x86_64-dev-20150828 - Platform: Linux 3.10.0-1127.el7.x86_64 Thank you and hope you will be able to help me resolve the issue. Isaac

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Problem_mri_watershed
by Edoardo Pinzuti 27 May '20

27 May '20

External Email - Use Caution Dear Freesurfer community, using the mri_watershed and -surf to crate inner_skull, outer_skin and outer_skull I get a incorrect inner_skull segmentation, probably due to an erroneous skullstrip. I tried to modify the parameters available but it does not help. Is there a way to correct this, manually correct or with a mask ? Any other suggestions will be really appreciated Thanks Edoardo

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PETsurfer: --usf in gtmseg
by Julie Ottoy 27 May '20

27 May '20

External Email - Use Caution Hi, In PETsurfer gtmseg, there is the --usf (upsampling factor) which is by default 2, corresponding to 0.5 mm voxelsize. I was wondering if the usf is recommended to be chosen depending on your mri voxelsize (eg, usf 1 for 1mm voxelsize of the mri), or will it just depend on how "accurate" you want your segmentation to be? Can you safely use --usf 2 for an mri with 1mm voxelsize? Thank you! best regards Julie

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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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