Freesurfer January 2018

freesurfer@nmr.mgh.harvard.edu

124 participants
195 discussions

funcroi-table-sess: how to specify frames for multi-band data
by Keishi NOMURA 03 Feb '18

03 Feb '18

Hi all, I’m using : freesurfer-Darwin-lion-stable-pub-v5.3.0 I’d like to plot HRF for each condition for each subject, using data acquired by multi-band EPI. Here are the commands I used: funcroi-config -roi rh.V1.roicfg -label rh.V1.label -analysis RH_fwhm8 -force funcroi-sess -s ORI01 -roi rh.V1.roicfg -df sessdirfile # m: frames foreach m ( 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 ) funcroi-table-sess -s ORI01 -df sessdirfile -roi rh.V1.roicfg -analysis RH_fwhm8 -c ASonlineRH -map cespct -o ./ROI/V1/ASonlineRH/ORI01.f$m.txt -frame $m end Then I got an error like “Error: input frame = 2, input volume only has 1 frames”. I referred to the related questions: https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg15883.html https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2011-April/017958.ht… It seems that there is nothing wrong with these commands, except for specifying the frames. One possibility is that using multi-band data is somehow causing trouble. I’m now using multi-band factor = 8 and TR = 0.8 sec, so then I set the frames to multiple number of TR = 0.8, and ran the commands again: foreach m ( 0.8 1.6 2.4 3.2 4.0 4.8 5.6 6.4 7.2 8.0 8.8 9.6 10.4 11.2 12.0 12.8 13.6 14.4 15.2 16 ) funcroi-table-sess -s ORI01 -df sessdirfile -roi rh.V1.roicfg -analysis RH_fwhm8 -c ASonlineRH -map cespct -o ./ROI/V1/ASonlineRH/ORI01.f$m.txt -frame $m end But still I get errors like “Error: input frame = 2, input volume only has 1 frames”. (when I used frame = 2.4. Hence, it seems that we cannot use non-integral inputs) So, my question is: (1) How should I specify frames when I use multi-band data? (2) Regarding (1), what temporal resolution do I get when I use TR = 0.8? (for example, TER = 0.8/20 = 0.04 or anything like that) (3) Or, is there anything wrong with my commands other than frames? Thank you, Keishi

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How to extract stats of the regions that is covered by large clusters
by Shatil, Anwar Shahadat 03 Feb '18

03 Feb '18

Hello Experts: After running mri_glmfit sim, I got below clusters: ClusterNo Max VtxMax Size(mm^2) MNIX MNIY MNIZ CWP CWPLow CWPHi NVtxs WghtVtx Annot 1 16.567 56197 13752.71 -36.8 -15.5 55.0 0.00020 0.00000 0.00040 30900 180209.80 precentral 2 9.630 57862 3018.98 -29.7 -72.0 -10.1 0.00020 0.00000 0.00040 4620 23119.05 fusiform 3 9.488 162470 2465.82 -16.0 -79.3 7.4 0.00020 0.00000 0.00040 4108 19097.47 pericalcarine 4 8.845 35506 1860.62 -24.5 -79.0 23.1 0.00020 0.00000 0.00040 3375 15122.28 superiorparietal 5 6.223 84246 1019.33 -4.8 15.4 -6.3 0.00020 0.00000 0.00040 1760 6950.26 rostralanteriorcingulate However, Cluster-1 area is large compared to others and it actually postcentral, and some portion of paracentral region. How can I extract the stats for these regions? Thanks, Anwar ------------------------------------------------ Anwar S. Shatil Research Assistant, Medical Imaging Sunnybrook Health Sciences Centre Toronto, ON, M4N 3M5 Email: anwar.shatil(a)sunnybrook.ca<mailto:anwar.shatil@sunnybrook.ca> This e-mail is intended only for the named recipient(s) and may contain confidential, personal and/or health information (information which may be subject to legal restrictions on use, retention and/or disclosure). No waiver of confidence is intended by virtue of communication via the internet. Any review or distribution by anyone other than the person(s) for whom it was originally intended is strictly prohibited. If you have received this e-mail in error, please contact the sender and destroy all copies.

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segmentHA_T2.sh
by Eva Hilland 02 Feb '18

02 Feb '18

Dear freesurfer experts, I have tried the dev version of Segmentation of hippocampal subfields and nuclei of the amygdala for OSX el Capitan, downloaded today. I did get an error message similar to a previous error I found on this mailing list: https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2017-November/054973… I have pasted the hippocampal-subfields-T2.HippoAMYT1andT2.log below Is this a matlab runtime problem? Many thanks in advance Eva -------------------------------------------- #@# Hippocampal Subfields processing (T1+T2) left Wed Jan 31 22:36:38 CET 2018 ------------------------------------------ Setting up environment variables --- DYLD_LIBRARY_PATH is .:/Applications/freesurfer/MCRv84//runtime/maci64:/Applications/freesurfer/MCRv84//bin/maci64:/Applications/freesurfer/MCRv84//sys/os/maci64: Invalid MEX-file '/tmp/MCR_4021793156/.mcrCache8.4/segmen0/autofs/space/panamint_005/users/iglesias/software/freesurfer.GEMS2.MAC/bin/kvlGEMSMatlab.mexmaci64': dlopen(/tmp/MCR_4021793156/.mcrCache8.4/segmen0/autofs/space/panamint_005/users/iglesias/software/freesurfer.GEMS2.MAC/bin/kvlGEMSMatlab.mexmaci64, 6): Symbol not found: __ZNKSt5ctypeIcE13_M_widen_initEv Referenced from: /tmp/MCR_4021793156/.mcrCache8.4/segmen0/autofs/space/panamint_005/users/iglesias/software/freesurfer.GEMS2.MAC/bin/kvlGEMSMatlab.mexmaci64 (which was built for Mac OS X 10.11) Expected in: /usr/lib/libstdc++.6.dylib in /tmp/MCR_4021793156/.mcrCache8.4/segmen0/autofs/space/panamint_005/users/iglesias/software/freesurfer.GEMS2.MAC/bin/kvlGEMSMatlab.mexmaci64 Error in kvlClear (line 11) Error in segmentSubjectT1T2_autoEstimateAlveusML (line 135) MATLAB:invalidMEXFile Darwin Evas-MacBook-Pro.local 15.5.0 Darwin Kernel Version 15.5.0: Tue Apr 19 18:36:36 PDT 2016; root:xnu-3248.50.21~8/RELEASE_X86_64 x86_64 T2 hippocampal subfields exited with ERRORS at Wed Jan 31 22:36:49 CET 2018

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Yendiki Anastasia config file
by Renew Andrade 31 Jan '18

31 Jan '18

Here is the configuration file. I think is the default by tutorial.

2 1

Issue with mri_convert on centOS 7
by Cooke,Danielle ( BIDMC - Neurology ) 31 Jan '18

31 Jan '18

Hello, I recently ran into issues using mri_convert on a CentOS 7 platform while having the same command work fine on CentOS 6. The error that results is: Segmentation fault (core dumped) I've tried on multiple machines with both operating systems to confirm the issue. I was wondering if you might have any insights or suggestions on how to fix this. Thank you! Danielle ________________________________ This message is intended for the use of the person(s) to whom it may be addressed. It may contain information that is privileged, confidential, or otherwise protected from disclosure under applicable law. If you are not the intended recipient, any dissemination, distribution, copying, or use of this information is prohibited. If you have received this message in error, please permanently delete it and immediately notify the sender. Thank you.

2 3

Longitudinal TRACULA study
by Donatas Sederevicius 31 Jan '18

31 Jan '18

Hi, I want to clarify some aspects longitudinal TRACULA processing before processing my data. For example, I have 3 timepoints of data of the same participant: sub101_01 sub101_02 sub101_03 All of these have structural and diffusion data (same scanner, same acquisition parameters). I processed structural data using FS longitudinal pipeline and got the following: base_101 sub101_01.long.base_101 sub101_02.long.base_101 sub101_03.long.base_101 Now I want to run longitudinal TRACULA processing. If all data is OK after quality checking (struct and DWI) I could set the configuration file as follows: set subjlist = ( sub101_01 \ sub101_02 \ sub101_03 ) set baselist = ( base_101 \ base_101 \ base_101 ) It turns out that DWI data of sub101_01 is extremely distorted and cannot be used for processing. Should I re-process struct data based on the last two timepoints or is it perfectly fine to use the base and long derived from all timepoints although I’m running tracula for the last two timepoints of DWI? In addition to that, is it fine to run longitudinal TRACULA on a list of subjects where some of them have only one timepoint of data and structural processing underwent longitudinal pipeline for that one timepoint? Thank you for your answers. Best, Donatas

1 0

annotation to volume with custom color scheme (Yeo parcellations)
by Dorit Kliemann 30 Jan '18

30 Jan '18

Hi, I’m trying to use the Yeo2011 annotations to create individual volume masks in subject space. I first use mri_surf2surf to map the annotations from fsaverage to individual subjects: mri_surf2surf --srcsubject fsaverage --trgsubject subject --hemi rh --sval-annot fsaverage/label/rh.Yeo2011_7Networks_N1000.annot --tval $SUBJECTS_DIR/subject/label/rh.Yeo2011_7Networks_N1000 Then I use mri_apar2aseg to map the annotation from the surface to the volume and thought he annot-table flag would use the labels provided in the custom color lut file. mri_aparc2aseg --s subject --o test.mgz --annot Yeo2011_7Networks_N1000 --annot-table path_to/Yeo2011_7Networks_ColorLUT.txt However the output is using different segmentation/color assignments. I can certainly find out which segmentation corresponds to which color and extract them separately (i.e. with fslmath or mri_binarize)..just wandering if I missed something or something changed since these posts? https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg35247.html Thanks Dorit

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Re: [Freesurfer] Strange Segmentation
by Antonin Skoch 30 Jan '18

30 Jan '18

Dear Arkadiy, I see sometimes these kind of errors. I think they are caused by local mis-segmentation due to WM hypointensities (enlarged perivascular spaces or other lesions, usually benign) located just under GM. Sometimes it is hard to discern where it is a hypointensity and where it is just a sulcus. I recommend to assess them using all 3 slice orientations. I correct them by editing wm.mgz (filling in voxels by value 255). Regards, Antonin Skoch Dear Experts, This brain looks a little bit strange to us, and I was wondering if someone might be able to chime in about whether this is worth editing, based on the screenshots of different slices from the sagittal view.. Thank you for your expertise. -Arkadiy

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A question about FS6 hippocampal subfield segmentation output file
by Darko Komnenić 30 Jan '18

30 Jan '18

Dear FreeSurfer experts, in the txt files [lr]h.hippoSfVolumes-T1.v10.txt we can see the volumes of individual hippocampal subfields - I was wondering what are the units in which volume is given? Millimeters cubic, voxels, or something else? Thanks in advance! Best, Darko

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Re: [Freesurfer] To Yendiki, Anastasia on TRACULA (Yendiki, Anastasia)
by Renew Andrade 30 Jan '18

30 Jan '18

What is the configuration file or where can I find it?

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Freesurfer January 2018