Freesurfer

freesurfer@nmr.mgh.harvard.edu

16 participants
30084 discussions

Resting state fMRI - volume analysis
by Wenzhen Zhao 07 Oct '20

07 Oct '20

External Email - Use Caution Dear Freesurfer Developers, I have a question regarding volume analysis of fMRI data. I wanted to perform volume analysis in MNI305 space, and I used following command after creating a seed; $mkanalysis-sess -analysis lh.pcc.mni305.vol -mni305 2 -stc siemens -fwhm 0 -notask -taskreg lh.pcc.dat 1 -nuisreg vcsf.dat 5 -nuisreg wm.dat 5 -mcextreg -polyfit 5 -nskip 10 -fsd rest -hpf 0.01 -TR 3 -per-run $selxavg3-sess -s sess01 -a lh.pcc.mni305.vol -no-preproc -overwrite The resulting analysis seems only showing subcortical regions, not the whole brain. (Shown in the attachment) I read on the page that volume analysis is only for subcortical regions, is this the reason that I only see subcortical regions? Another problem is that in the preprocessing step, I could not smooth the volume. If I do, it seems to distort the image and only gives something similar to the picture shown. Could this be the reason for the distorted analysis? Thanks for your help. Best, Wenzhen

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Recon-all Results for fMRI
by goktekin.durusoy＠boun.edu.tr 07 Oct '20

07 Oct '20

External Email - Use Caution Hi, I am using freesurfer 5.3.0. I would like to ask whether it is possible or not to have different results for destrieux atlas parcellation for the same data. (aparc.a2009s+aseg.mgz file). It seems there is a little difference in terms of parcellation locations and their volumes. Thank you, Goktekin Durusoy

2 3

create .nv or .pial file with atlas based values
by Xin Niu 07 Oct '20

07 Oct '20

External Email - Use Caution Dear freesurfer experts, We have some files containing the values for regions based on the Deskian/Killiany atlas like : ROI, value 'lh_bankssts', .9 'lh_caudalanteriorcingulate', .1 'lh_caudalmiddlefrontal', .5 'lh_cuneus', .2 'lh_entorhinal', .5 'lh_fusiform', .9 'lh_inferiorparietal', .7 And we have the information on the labels in Matlab data format: [image: image.png] I wish to create a surface file (.nv or .pial) based on the atlas and values which can be visualized directly in software like BrainNetViewer. We are also considering to visualized the brain images with SurfStat which needs a .obj file and .txt file: s100 = SurfStatReadSurf( {... 'c:/keith/fMRI/ICBM/surfaces/mni_icbm_00100_mid_surface_left_81920.obj',... 'c:/keith/fMRI/ICBM/surfaces/mni_icbm_00100_mid_surface_right_81920.obj'} ); t100 = SurfStatReadData( {... 'c:/keith/fMRI/ICBM/thickness/mni_icbm_00100_native_rms_rsl_tlink_20mm_left.txt',... 'c:/keith/fMRI/ICBM/thickness/mni_icbm_00100_native_rms_rsl_tlink_20mm_right.txt'} ); SurfStatView( t100, s100, 'Cort Thick (mm), Subj 00100' ); But I have no idea how the .obj file is created and how the .txt file should be organized. Is there any way to make it? Thanks in advance! Best, Xin Xin Niu Drexel University, Department of Psychology Stratton Hall 314 3201 Chestnut Street Philadelphia, PA 19104

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recon-all -s <subject> -autorecon2-cp -autorecon3 error
by Kazuki Sakakura 07 Oct '20

07 Oct '20

External Email - Use Caution Hello FreeSurfer Developers, I'm attempting to compute recon-all after putting control point, but for some of my subjects I get the attached error when I run the recon-all -s <subject> -autorecon2-cp -autorecon3 command. I've searched the list and no similar errors have been reported. Does anyone have any thoughts on how to trouble-shoot this one? Also, Ive attached the recon-all.log in case it's of any use. 1) FreeSurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 2) Platform: Ubuuntu 14.04 3) recon-all.log: see attached Best Regards, Kazuki Sakakura

2 1

qdec problems not receiving keyboard input
by Agurne Sampedro Calvete 07 Oct '20

07 Oct '20

External Email - Use Caution Dear Freesurfer Experts, Although I haven't had any problems with the qdec until now, this week the qdec is having some errors when receiving inputs from the keyboard. For example, I can't write in the design name box, nor can I change the minimum or maximum threshold in the display page. I've seen that other people have had a similar problem too. How can I solve it? Thanks in advance. Kind regards, Agurne Sampedro

2 1

Turn off bias field correction for SAMSEG
by Donatas Sederevicius 06 Oct '20

06 Oct '20

External Email - Use Caution Dear FreeSurfer team, Is there a way to turn off the bias field estimation and correction while running SAMSEG? I have images that are bias field corrected and would be great to skip this extra bias field estimation. Thanks in advance. Best, Donatas

2 1

Lobe segmentation
by Platten, Michael 06 Oct '20

06 Oct '20

Hi, I have a question regarding lobe (temporal, frontal, parietal, and occipital) segmentation. I have already completed a recon-all for all subjects. I have seen that the surface stream has a -lobesStrict function which parcellates the lobes. I have also seen that you can convert the surface to a volume through mri_surf2vol. This, I believe, would in the end get me what I'm after; which are the lobe segmentations. My plan is to overlay a lesion mask and extract the lesions based on, among other things, which lobe they belong to. I was wondering if there was a way to use the segmentation outputs from FreeSurfer to get lobe segmentation directly, i.e. by adding up various segmentation volumes? Or do I have to go through the Surface stream? Is my above-stated method the easiest and best way to get lobe segmentations in order to extract the lesion load per lobe? Thank you for your time and help! Best, Michael

2 1

Parallel Run of Multiple Patients
by gunes 06 Oct '20

06 Oct '20

External Email - Use Caution Dear Freesurfer experts, We have a pipeline script that uses *recon-all* and other executables (like applywarp, mri_convert, mri_em_register etc.) several times. We ran our script in parallel from different terminals to process the patients faster. However, it's come to our attention that the directory *$FREESURFER_HOME/subjects* is being used by *recon-all* and other scripts in common. So, if we run our pipeline script in parallel, they'll call *recon-all* and other freesurfer scripts in parallel, possibly writing to and reading from this directory, eventually leading to a mix up in the patient data. So, we feel that we need to run our script one by one for the patients. Am I right to be concerned about this? Kind Regards, Gunes

3 3

Issues with transferring edits from v6.0dev into v7.1
by Melanie Ganz 06 Oct '20

06 Oct '20

External Email - Use Caution Dear FS list, as soon as samseg was available in FS v6dev we used it to process some of our data. The plan was always to wait for v7 to use a stable version, but edits were made already on v6FSdev, while we waited last spring for v7 to come out. Now I have been having issues with transferring edits from v6dev into v7.1, which I thought should be a straight forward thing to do. The way I did it, is I ran v7.1 on the raw data, then I copied the files where edits where made, e.g. brainmask.mgz, wm.mgz as well as control.dat. Finally, at this point I reran recon-all -all ( since I actually couldn't get recon-all with the -make flag to work). But I see my rerun fails with the error message: Saving brainmask.auto.mgz Command terminated by signal 11 @#@FSTIME 2020:10:06:14:45:45 mri_watershed N 10 e 20.81 S 1.93 U 22.55 P 117% M 893740 F 0 R 330549 W 0 c 83 w 1353 I 22344 O 2312 L 3.35 3.67 2.94 @#@FSLOADPOST 2020:10:06:14:46:06 mri_watershed N 10 3.10 3.59 2.93 Linux krogh 4.12.14-lp151.28.59-default #1 SMP Wed Aug 5 10:58:34 UTC 2020 (337e42e) x86_64 x86_64 x86_64 GNU/Linux recon-all -s g612_GD exited with ERRORS at Tue Oct 6 14:46:06 CEST 2020 and I don't understand why. The earlier FSrun with v7.1 ran fine and I also tried copying to a separate directory to check file permissions and the same error appears again. I have uploaded the subject to the ftp server at surfer.nmr.mgh.harvard.edu and it's called subject.tar.gz. Kind regards, Melanie -- Yours sincerely Melanie Ganz-Benjaminsen Forsker Direct: + 45 35 45 67 18 Mail: melanie.ganz(a)nru.dk Neurobiology Research Unit Rigshospitalet, building 6931 Juliane Maries Vej 28, 3rd floor DK-2100 Copenhagen, Denmark Phone: +45 3545 6712 Fax: +45 3545 6713 URL:http://nru.dk This e-mail and any attachment may contain confidential and privileged material intended for the addressee only. If you are not the addressee, you are notified that no part of the e-mail or any attachment may be disclosed, copied or distributed, and that any other action related to this e-mail or attachment is strictly prohibited, and may be unlawful. If you have received this e-mail by error, please notify the sender immediately by return e-mail, and delete this message.

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[WARNING: UNSCANNABLE EXTRACTION FAILED]Macaque brain segmentation
by Jie Zhao 06 Oct '20

06 Oct '20

External Email - Use Caution Hello Freesurfer Team I am trying to segment the macaque brain. After skull strip, control point adding and white matter editing, I try to inflate the brain surface. My command is :recon-all -s monkey2 -autorecon2-wm -noaseg -cc-crs 100 85 112 -pons-crs 99 105 80 The output error is: #@# WhitePreAparc lh 2020年 10月 05日星期一 13:23:44 CST cd /usr/local/freesurfer/subjects/monkey2/mri mris_place_surface --adgws-in ../surf/autodet.gw.stats.lh.dat --wm wm.mgz --invol brain.finalsurfs.mgz --lh --i ../surf/lh.orig --o ../surf/lh.white.preaparc --white --nsmooth 5 7.1.0 7.1.0 cd /usr/local/freesurfer/subjects/monkey2/mri setenv SUBJECTS_DIR /usr/local/freesurfer/subjects mris_place_surface --adgws-in ../surf/autodet.gw.stats.lh.dat --wm wm.mgz --invol brain.finalsurfs.mgz --lh --i ../surf/lh.orig --o ../surf/lh.white.preaparc --white --nsmooth 5 Reading in input surface ../surf/lh.orig Smoothing surface with 5 iterations Area 230166 0.28728 0.06614 0.000899 0.5852 Corner 690498 60.00000 9.22592 3.263084 157.1301 Edge 345249 0.81774 0.11586 0.028436 1.5900 Hinge 345249 4.79409 6.13323 0.000002 153.5438 Not reading in aparc Reading in input volume brain.finalsurfs.mgz Reading in wm volume wm.mgz MRIclipBrightWM(): nthresh=30761, wmmin=5, clip=110 MRIfindBrightNonWM(): 6937 bright non-wm voxels segmented. Masking bright non-wm for white surface MRImask(): AllowDiffGeom = 1 MRImask(): AllowDiffGeom = 1 Ripping frozen voxels ERROR: need seg for ripping Command exited with non-zero status 1 @#@FSTIME 2020:10:05:13:23:44 mris_place_surface N 14 e 12.39 S 0.16 U 10.80 P 88% M 434260 F 25 R 126035 W 0 c 3134 w 27 I 5168 O 0 L 1.41 1.59 1.40 @#@FSLOADPOST 2020:10:05:13:23:56 mris_place_surface N 14 1.32 1.56 1.39 Linux zhao-VirtualBox 4.15.0-118-generic #119-Ubuntu SMP Tue Sep 8 12:30:01 UTC 2020 x86_64 x86_64 x86_64 GNU/Linux Can you help me explain above error and how to solve this problem? I have attached the wm.mgz,but recon-all.log and brainmask.mgz are beyond the size limit . Thanks in advance! All best, Jie

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