Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30058 discussions

Re: [Freesurfer] recon-all error
by Bruce Fischl 23 Jan '18

23 Jan '18

we don't have much experience with it. Can you cc the FS list so that others can answer? I'll do so on this email. Maybe try some other tool for conversion? If recon-all fails it is not surprising that mri_convert also fails since they use the same DICOM code cheers Bruce On Tue, 23 Jan 2018, Julia Ströhlein wrote: > > Hi Bruce, > > thank you very much for your reply. > > > > I’m sure that I use the right series. I tried to convert my DICOM files to > nifti, but this produces > the same error and the command also doesn`t create the NIFTI file. > > > > Julias-MacBook-Air:~ Jule$ cd > /Applications/freesurfer/subjects/MRtest2/001/001/9 > > Julias-MacBook-Air:9 Jule$ mri_convert 00010001 00010001.nii > > mri_convert.bin 00010001 00010001.nii > > $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ > > reading from 00010001... > > Starting DICOMRead2() > > dcmfile = /Applications/freesurfer/subjects/MRtest2/001/001/9/00010001 > > dcmdir = /Applications/freesurfer/subjects/MRtest2/001/001/9 > > ERROR: don't know how to get DWI parameters from --Hitachi Medical > Corporation -- > > ERROR: GetDICOMInfo(): dcmGetDWIParams() 1 > > DICOM File: /Applications/freesurfer/subjects/MRtest2/001/001/9/00010001 > > break DICOMRead.c:5228 > > Ref Series No = 9 > > Found 302 files, checking for dicoms > > ERROR: don't know how to get DWI parameters from --Hitachi Medical > Corporation – > > > > Do you know problems like this with this type of MR scanner? > > > > Kind regards, > > Julia > > > > Unbenannt > > > > >

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Re: [Freesurfer] [Re] medial wall label in Freesurfer 6
by M del Mar Velasco 23 Jan '18

23 Jan '18

Yes, it solves medial_wall label problem but not mri_aparc2aseg error.log. I attached you in a previous message: https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg56610.html Many thanks, M del Mar

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Re: [Freesurfer] MRI protocol for hippocampal subfield segmentation
by Gabor Perlaki 23 Jan '18

23 Jan '18

Dear Iglesias, Do you think that it is useful to also use a fieldmap for hippocampal subfield segmentation? Can Freesurfer's hippocampal subfield segmentation use it? I'm not sure that due to the limited resolution of the fieldmap and due to registration issues it is worth to acquire a fieldmap for hippocampal subfield segmentation. What do you think? Best, Gabor

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Inquiry about process time by use "recon-all"
by Ritthikrai Thaweecharoen 23 Jan '18

23 Jan '18

Dear FreeSurfer Staff, We have conducted a brain volume study in normal Thai elderly. We found that the process time to analyze the brain of 20% of our subject took over 40 hours. The maximum process time is 99 hours. Eventhough the size of imaging file is around 20 MB and use “recon -all” command to process file. It would be grateful if you could help to explain tedious process time of FreeSurfer and how to shorten this process time. Our Machine spec. is as following: • INTEL i5 – 4260U CPU(a)1.4GHz • RAM 8 MB • Cent OS 6.x Best Regards Ritthikrai Thaweecharoen Data Scientist Research and Development Department Tel: 02 755 1919 Email Disclaimer : The information contained in this electronic mail message may be confidential and protected information intended only for the use of the entity name above. As the recipient of this information you may be prohibited by law from disclosing this information to any other parties without specific written authorization from the individual to whom it pertains. If the reader of this message is not the intended recipient, or the employee or agent responsible for delivering it to the intended recipient, you are hereby notified that any disclosure, dissemination, distribution, copying, or action taken in reliance on the contents of this communication is strictly prohibited, If you have received this communication in error, please notify me back immediately by telephone and destroy the message and its attachments.

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freesurfer bids app cannot find license file
by Dianne Patterson 22 Jan '18

22 Jan '18

After trying the example bids app (which worked fine), I am trying the freesurfer bids app: https://github.com/BIDS-Apps/freesurfer I have built the docker container on my mac and I have the ds005 data directory here and the license.txt which I requested from freesurfer. I asked for a linux license (assuming the container contains linux and that was the relevant fact). dpat@Saci:/Volumes/Main/Working/BIDS_TESTING% docker run -ti --rm -v /Volumes/Main/Working/BIDS_TESTING/ds005:/bids_dataset:ro -v /Volumes/Main/Working/BIDS_TESTING/outputs:/outputs bids/freesurfer /bids_dataset /outputs participant --license_file "license.txt" 1: You should define 'SliceTiming' for this file. If you don't provide this information slice time correction will not be possible. (code: 13 - SLICE_TIMING_NOT_DEFINED) /sub-01/func/sub-01_task-mixedgamblestask_run-01_bold.nii.gz /sub-01/func/sub-01_task-mixedgamblestask_run-02_bold.nii.gz /sub-01/func/sub-01_task-mixedgamblestask_run-03_bold.nii.gz /sub-02/func/sub-02_task-mixedgamblestask_run-01_bold.nii.gz /sub-02/func/sub-02_task-mixedgamblestask_run-02_bold.nii.gz /sub-02/func/sub-02_task-mixedgamblestask_run-03_bold.nii.gz /sub-03/func/sub-03_task-mixedgamblestask_run-01_bold.nii.gz /sub-03/func/sub-03_task-mixedgamblestask_run-02_bold.nii.gz /sub-03/func/sub-03_task-mixedgamblestask_run-03_bold.nii.gz /sub-04/func/sub-04_task-mixedgamblestask_run-01_bold.nii.gz ... and 38 more files having this issue (Use --verbose to see them all). Summary: Available Tasks: Available Modalities: 133 Files, 1.77GB mixed-gambles task T1w 16 - Subjects inplaneT2 1 - Session bold Traceback (most recent call last): File "/run.py", line 165, in <module> raise Exception("Provided license file does not exist") *Exception: Provided license file does not exist* =========== If I provide the full path to the license file, it still fails: docker run -ti --rm -v /Volumes/Main/Working/BIDS_TESTING/ds005:/bids_dataset:ro -v /Volumes/Main/Working/BIDS_TESTING/outputs:/outputs bids/freesurfer /bids_dataset /outputs participant --license_file "/Volumes/Main/Working/BIDS_ TESTING/license.txt" Suggestions? How do I tell freesurfer where the license file is? Thanks so much, Dianne -- Dianne Patterson, Ph.D. Research Scientist dkp(a)email.arizona.edu <dkp(a)u.arizona.edu> or diannepat(a)gmail.com University of Arizona Speech and Hearing Science 314 1131 E 2nd Street, Building #71 (Just East of Harvill) ============== If you don't hear back from me (and you expected to), I blame the University's new SPAM filter. Please write to my gmail account. ============== Antipiphany: That moment when you realize how little you actually know ============== -- Dianne Patterson, Ph.D. Research Scientist dkp(a)email.arizona.edu <dkp(a)u.arizona.edu> or diannepat(a)gmail.com University of Arizona Speech and Hearing Science 314 1131 E 2nd Street, Building #71 (Just East of Harvill) ============== If you don't hear back from me (and you expected to), I blame the University's new SPAM filter. Please write to my gmail account. ============== Antipiphany: That moment when you realize how little you actually know ==============

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Re: [Freesurfer] TRACULA QC
by Yendiki, Anastasia 22 Jan '18

22 Jan '18

Hi Linnea – Before the stats are computed, the probability distribution of the paths is thresholded to 20% of its peak value, so voxels with very low probability will not affect the outcome. Best, a.y From: <freesurfer-bounces(a)nmr.mgh.harvard.edu<mailto:freesurfer-bounces@nmr.mgh.harvard.edu>> on behalf of Linnea Marie Dramdal Borg <lmborg(a)stud.ntnu.no<mailto:lmborg@stud.ntnu.no>> Reply-To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> Date: Monday, January 22, 2018 at 10:26 AM To: "freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>" <freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> Subject: [Freesurfer] TRACULA QC Hi, We have run into some issues with our tractographies. I have attached examples: In "fmajor_4053.png", there is a "bridge" in forceps minor on its way to the frontal lobe. We've also come across other cases of bridging in forceps minor, such as "fminor_4013". Also, there are some voxel paths that are rather weak, such as "unc_2068_1.png" and "unc_3022_1.png"/"unc_3022_2.png". This does not seem optimal. Do you agree? We've also come across a couple of cases where it hasn't really found the tract correctly, such as in "29_ccg_1", "unc_3045_1.png" and "268_ccg.png". This also includes "fmm_32.png", which has a nice voxel intensity, but neither the forceps minor nor major voxels really fit their underlying tracts. Finally, neither "unc_3068_2.png" nor "unc_4040.png" are really correct. Should we reinitialize all of them, or can we use some of them without affecting the results too much? Thank you, Linnea Marie

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FreeSurfer Installation
by Caio Quini 22 Jan '18

22 Jan '18

Hello I am trying to download FreeSurfer from freesurfer.net and I can't open the download page. It keeps returning an error message. Is that a common error? Is there any other way to download the software? Thank you very much. Regards Caio Quini

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Anatomical ROI analysis
by Ting Li 22 Jan '18

22 Jan '18

Hi, all experts, I am studying the AnatomicalROIV6.0 tutorials. In the Anatomical ROI analysis tutorial, the first four part work well. While in the Group stats files, I got an error information like this. group_analysis_tutorial ting$ asegstats2table --subjects 004 021 040 067 080 092 \ > --segno 11 17 18 \ > --tablefile aseg.vol.table File "/Applications/freesurfer/bin/asegstats2table", line 195 print 'ERROR: subjects are not specified (use --subjects SUBJECTS)' ^ SyntaxError: invalid syntax Thanks for your help. Ting

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recon-all error
by "Julia Ströhlein" 22 Jan '18

22 Jan '18

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Hippocampal subfields segmentation
by Alexis Guyot 22 Jan '18

22 Jan '18

Dear Freesurfer developers, I have been trying to segment (with Freesurfer v6.0.0, on Ubuntu 14.04) the hippocampal subfields of two 7T MR images in NIFTI format: an isotropic (0.8*0.8*0.8 mm3) whole-brain T1-weighted source volume with an anisotropic (0.3*1.2*0.3 mm3) T2-weighted volume covering the brain partially and centred on a region comprising both hippocampi. I have followed the instructions in https://surfer.nmr.mgh. harvard.edu/fswiki/HighFieldRecon to correct the bias in the two 7T volumes ('T1_biasCorrected.png', 'T2_biasCorrected.png'). I have run 'recon-all -hires [...] -expert expert.txt' ('expert.txt') on my bias-corrected T1 volume, which produced an accurate segmentation ('aseg.png', 'recon-all.log'). Following this, I have run 'recon-all -hippocampal-subfields-T2' on the bias-corrected T2 volume ('hippocampal-subfields-T2.log'). Looking at the resulting segmentation, I am unsure the molecular layer has been properly delineated in the body of the hippocampus ('right_hippocampus_body.png', 'right_hippocampus_body_seg.png'). In addition, it appears the convolutions in the hippocampal head have not been correctly segmented ('right_hippocampus_head.png', 'right_hippocampus_head_seg.png'). I am not certain this is the expected behaviour when running the hippocampal subfields module on high-res data. Is it possible the recon-all output is not accurate enough (should I adjust the mres_inflate value prior to segmenting the brain)? Could the high anisotropy of the T2 volume hinder the segmentation process? Any thoughts on this? Screenshots/attachments are available on request, as my previous message was rejected for being too big. Thanks for your help, Alexis

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