Freesurfer September 2020

freesurfer@nmr.mgh.harvard.edu

111 participants
165 discussions

Re: [Freesurfer] big difference between ICV same patient....
by Gonzalo Rojas Costa 15 Sep '20

15 Sep '20

External Email - Use Caution Hi: I modified the coregistration using "tkregister2 --s subj1 --fstal --surfs". Then, I used "recon-all -make all -s subj1", but I got "Nothing to be done"... why ?... Which command must I run after tkregister2 to reprocess ? Other question... what do you mean with " You might be comparing dewarped vs not dewarped" Sincerely, Gonzalo Rojas Costa >Message: 6 >Date: Thu, 10 Sep 2020 12:42:41 -0400 >From: "Douglas N. Greve" <dgreve(a)mgh.harvard.edu> >Subject: Re: [Freesurfer] big difference between ICV same patient.... >To: <freesurfer(a)nmr.mgh.harvard.edu> >Message-ID: <0112a2be-2c41-a100-6ac7-e8d054e970eb(a)mgh.harvard.edu> >Content-Type: text/plain; charset="utf-8" > >It all comes down to the registration. See >https://surfer.nmr.mgh.harvard.edu/fswiki/eTIV >The image may have more-or-less neck and that can change the >registration and ICV. The contrast may be different. The scanner may >have had software updates. You might be comparing dewarped vs not dewarped. > >On 9/10/2020 2:16 PM, Gonzalo Rojas Costa wrote: >> >> ????????External Email - Use Caution >> >> Hi: >> >> ? Why I got a big ICV difference between MPRAGE of the same patient >> (2019: 1775887.317631, 2020: 1566398.53576 mm3), one-year difference >> acquisition, and the same MRI Skyra 3T equipment? I used freesurfer >> 5.1.0 on the same computer, and operating system in both cases... >> >> ? I reviewed the coregistration to MNI305 and it is reasonably good in >> both cases... >> >> ? The case was reviewed by an expert neuroradiologist, and she does >> not consider that there is a significant visual difference between >> both sizes. >> >> ? Sincerely >> >> >> >> Gonzalo Rojas Costa

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ERROR | License file for FS 7.1
by Otília C. d'Almeida 15 Sep '20

15 Sep '20

External Email - Use Caution Hi, I'm struggling to use tkmedit with FreeSurfer 7.1. For example, trying: tkmedit SUBJECT brainmask.mgz -surfs The error message I got is: ------ GNU libc version:2.19 ERROR: Systems running GNU glibc version greater than 2.15 require a newly formatted license file (it's free). Please download a new one from the following page: ..../registration.html ------ All the registration steps were performed, and a license.txt file was sent. This file was copied to $FREESURFER_HOME. The problem remains. Anyone had the same issue? How did you solve it? Also, here https://surfer.nmr.mgh.harvard.edu/fswiki/LinuxInstall it is said that the license.txt file have 3 lines. The info sent have more since the e-mail is also included. What is the format of the license file? Thank you! with kind regards, Otília

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Segmentation of hippocampus and amygdala: using an additional scan with low-pixel
by 최선아 / 학생 / 뇌인지과학과 14 Sep '20

14 Sep '20

External Email - Use Caution Hello FreeSurfer Developers, I am attempting a quality check for my segmentation using an additional scan. My segmentation of hippocampal subfields and nuclei of the amygdala using an additional scan were successfully done. However, I am not sure it is better to use an additional scan since its pixel density is low. I used a T1 image with 0.977*0.977*1(mm, x*y*z axis) pixel, and T2 FLAIR image with 0.688*0.688*6(mm, x*y*z axis) pixel. *Is it okay to use an additional scan having a big pixel size such as 6mm? Can I still say that the segmentation with the additional scan is more reliable than solely using a T1 scan?* I checked the outputs using freeview, but it was difficult to conclude. 1) Freesurfer version: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b 2) Platform: Ubuntu 18.04 LTS Thanks for your help. Thanks. Sunah.

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recon-all -s BIO-ALS-701-005-BL exited with ERRORS
by Zaninotto, Ana Luiza Costa 14 Sep '20

14 Sep '20

Dear developers, I have been trying to run the recon-all without success. I am working remotely using my Windows laptop through NoMachine Linux. Please see below the scripts and the error message. Thank you. epimetheus:alz14[854] recon-all -i /autofs/cluster/atassigp/ALSspeech/BIO-ALS-701-005-BL/MPRAGE/005/78000-000005-000001.dcm -subject BIO-ALS-701-005-BL -all -brainstem-structures Subject Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c Current Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c INFO: SUBJECTS_DIR is /autofs/cluster/atassigp/ALSspeech/FS/Subjects Actual FREESURFER_HOME /autofs/cluster/freesurfer/centos6_x86_64/stable6_0_0 Linux epimetheus.nmr.mgh.harvard.edu 3.10.0-1062.4.3.el7.x86_64 #1 SMP Wed Nov 13 23:58:53 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux '/autofs/cluster/freesurfer/centos6_x86_64/stable6_0_0/bin/recon-all' -> '/autofs/cluster/atassigp/ALSspeech/FS/Subjects/BIO-ALS-701-005-BL/scripts/recon-all.local-copy' /autofs/cluster/atassigp/ALSspeech/FS/Subjects/BIO-ALS-701-005-BL mri_convert /autofs/cluster/atassigp/ALSspeech/BIO-ALS-701-005-BL/MPRAGE/005/78000-000005-000001.dcm /autofs/cluster/atassigp/ALSspeech/FS/Subjects/BIO-ALS-701-005-BL/mri/orig/001.mgz mri_convert.bin /autofs/cluster/atassigp/ALSspeech/BIO-ALS-701-005-BL/MPRAGE/005/78000-000005-000001.dcm /autofs/cluster/atassigp/ALSspeech/FS/Subjects/BIO-ALS-701-005-BL/mri/orig/001.mgz $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from /autofs/cluster/atassigp/ALSspeech/BIO-ALS-701-005-BL/MPRAGE/005/78000-000005-000001.dcm... Getting Series No INFO: Found 719 files in /autofs/cluster/atassigp/ALSspeech/BIO-ALS-701-005-BL/MPRAGE/005 INFO: Scanning for Series Number 5 Scanning Directory INFO: found 704 files in series INFO: loading series header info. RunNo = 4 INFO: sorting. sdfiSameSlicePos() eps = 0.000001 INFO: (256 256 176), nframes = 4, ismosaic=0 sdfi->UseSliceScaleFactor 0 datatype = 4, short=4, float=3 PE Dir ROW ROW AutoAlign matrix detected AutoAlign Matrix --------------------- 0.98640 0.09502 -0.13409 -22.58164; -0.07808 0.98890 0.12638 16.16202; 0.14461 -0.11420 0.98288 -7.16005; 0.00000 0.00000 0.00000 1.00000; FileName /autofs/cluster/atassigp/ALSspeech/BIO-ALS-701-005-BL/MPRAGE/005/78000-000005-000001.dcm Identification NumarisVer syngo MR B13 4VB13A ScannerModel TrioTim PatientName HUP_PBR03_ALS701-005_120604 Date and time StudyDate 20120604 StudyTime 104553.448000 SeriesTime 110830.078000 AcqTime 110221.415000 Acquisition parameters PulseSeq tfl3d4_ns Protocol MEMPRAGE_4e_p3_1mm_iso PhEncDir ROW EchoNo 1 FlipAngle 7 EchoTime 1.64 InversionTime 1200 RepetitionTime 2530 PhEncFOV 256 ReadoutFOV 256 Image information RunNo 4 SeriesNo 5 ImageNo 1 NImageRows 256 NImageCols 256 NFrames 4 SliceArraylSize 1 IsMosaic 0 ImgPos 137.3315 96.1324 107.3163 VolRes 1.0000 1.0000 1.0000 VolDim 256 256 176 Vc -0.0950 -0.9889 -0.1142 Vr -0.1341 0.1264 -0.9829 Vs -0.9864 0.0781 0.1446 VolCenter 21.2017 -7.3992 -20.3829 TransferSyntaxUID 1.2.840.10008.1.2.1 UseSliceScaleFactor 0 (slice 0: 1) IsDWI = 0 INFO: no Siemens slice order reversal detected (good!). TR=2530.00, TE=1.64, TI=1200.00, flip angle=7.00 i_ras = (-0.095018, -0.988904, -0.114196) j_ras = (-0.134094, 0.126384, -0.982876) k_ras = (-0.986403, 0.078078, 0.144615) writing to /autofs/cluster/atassigp/ALSspeech/FS/Subjects/BIO-ALS-701-005-BL/mri/orig/001.mgz... #-------------------------------------------- #@# MotionCor Mon Sep 14 14:11:28 EDT 2020 Found 1 runs /autofs/cluster/atassigp/ALSspeech/FS/Subjects/BIO-ALS-701-005-BL/mri/orig/001.mgz Checking for (invalid) multi-frame inputs... ERROR: input(s) cannot have multiple frames! /autofs/cluster/atassigp/ALSspeech/FS/Subjects/BIO-ALS-701-005-BL/mri/orig/001.mgz has 4 frames If this is a multi-frame MEMPRAGE image, use mri_concat --rms to combine echo frames. Linux epimetheus.nmr.mgh.harvard.edu 3.10.0-1062.4.3.el7.x86_64 #1 SMP Wed Nov 13 23:58:53 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux recon-all -s BIO-ALS-701-005-BL exited with ERRORS at Mon Sep 14 14:11:29 EDT 2020 For more details, see the log file /autofs/cluster/atassigp/ALSspeech/FS/Subjects/BIO-ALS-701-005-BL/scripts/recon-all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting Ana Luiza Zaninotto, B.A, MSc, Ph.D. Speech and Feeding Disorders Lab MGH Institute of Health Professions - MGHIHP +1 (617) 724-6347<https://www.google.com/search?q=speech+and+feeding+disorders+lab&rlz=1C1GCE…>, +1(857)294-2080 [cid:9097102c-a1f0-4411-8009-6508f44e67d6]

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Download of Freesurfer 7.1.1. and 7.1.0. continuously stalled
by Pien Jellema 14 Sep '20

14 Sep '20

External Email - Use Caution Hi all, I have been trying to download freesurfer 7.1.1 on my mac. However, each attempt stalls 1 MB before it is done. I had the exact same problem with version 7.1.0. There should be more than enough space on my external hard drive to install the program on. So I don’t understand what is going wrong. Some advice would be greatly appreciated. Kind regards, Sophie

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HIppocampal segmentation failure with FS 7.1.1
by Mukaino Takahiko 12 Sep '20

12 Sep '20

External Email - Use Caution Dear experts, I'm currently using FS 7.1.1 and have already done hippocampal segmentation with segmentHA_T2.sh command for over 100 subjects. Most results are excellent but some segmentations are inaccurate, for example, including neighbouring white and gray matter as CA1, even though T2 images are clear enough and the pial surface results show recon-all has successfully segmented hippocampus and parahippocampal gyrus. I'm wondering if there is any way to fix them, but I couldn't find any official writing to deal with this issue. Is there any method to fix this? Or the only way is to exclude these subjects? Best regards, Taka

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Asymmetry whole thalamus with native vs Iglesias method
by Chris Vriend 11 Sep '20

11 Sep '20

External Email - Use Caution Dear freesurfer experts, I’m currently using FreeSurfer 7.1 with the thalamus subsegmentation from Iglesias et al (version 12) to subsegment the thalamus. Something we noticed is that the asymmetry between the left and right whole thalamus is reversed when comparing the native thalamus segmentation by FreeSurfer itself and the Iglesias method. This is exemplified by the values below where we calculated the Asymmetry Index [ (Left – right)/(left + right) * 100 ] and shows that for some subjects the left thalamus is larger when looking at the results of the Iglesias method, but smaller with the native method. To allow comparison between the two methods we subtracted the LGN and MGN volumes from the whole thalamus volume, because – if I’m not mistaken – these nuclei are not segmented by the standard recon-all pipeline? We don’t know why we observe this and not just in one dataset or one subject but in multiple. Do you have any words of wisdom or explanation for this phenomenon? Your advice is much appreciated. Kind regards, Chris Vriend Whole_thalamus_lh_Iglesias whole_thalamus_rh_Iglesias AI Fsnative_Left-Thal Fsnative_Right-Thal AI 4913.391 5129.889 -2.155650345 5987.2 5764.6 1.894177913 6019.185 6235.017 -1.761289719 6793.9 6732.4 0.454669791 6374.575 6574.893 -1.546920692 7543.9 7592.1 -0.318446089 6974.051 6983.314 -0.066366395 7661.3 7624.8 0.238779021 5907.853 5798.037 0.93812602 6756.4 6485.2 2.048090865 6316.792 6382.639 -0.518503546 7191.2 6959.7 1.63593835

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Re: [Freesurfer] Updating Freesurfer Version
by Ferraro, Pilar 10 Sep '20

10 Sep '20

External Email - Use Caution Hi Freesurfer experts, I’m trying to update my current Freesurfer version (from 6.0 to 7.1). I’d like to know whether the installation procedure for 7.1 would overwrite the current one (6.0). Many thanks, Pilar > Il giorno 22 ago 2020, alle ore 7:48 AM, freesurfer-request(a)nmr.mgh.harvard.edu ha scritto: > > 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. Global surface area and global thickness values (Palin, Tara) > 2. How to run recon-all for different subjects and each subject > with different sessions ? (Camargo, Aldo) > 3. Postdoctoral scientist positions at UCSF (Tosun, Duygu) > 4. Re: extracting beta coefficients and p-values (Douglas N. Greve) > 5. Re: How to run recon-all for different subjects and each > subject with different sessions ? (Douglas N. Greve) > 6. Re: Global surface area and global thickness values > (Douglas N. Greve) > 7. Re: ROI-wide cortical thickness for each network ! (Martin Juneja) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Fri, 21 Aug 2020 18:55:16 +0000 > From: "Palin, Tara" <Palin(a)kennedykrieger.org> > Subject: [Freesurfer] Global surface area and global thickness values > To: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> > Cc: "Plotkin, Micah" <PlotkinMic(a)kennedykrieger.org>, "Crocetti, > Deana" <crocetti(a)kennedykrieger.org> > Message-ID: <162876d303f44e7d987ab303c0a11b45(a)kennedykrieger.org> > Content-Type: text/plain; charset="iso-8859-1" > > External Email - Use Caution > > Hello freesurfer experts, > > > I am looking to extract the global surface and global thickness measurements and am curious if my understanding of the output on the aparc.stats (for lh and rh) are correct. When looking at these files, at the very top you will find the Pial Surface Total Area and a Mean Thickness value which I am assuming are the global measures. Below you have all of the ROIs listed (this was not changed by us or generated by us this is what comes out of freesurfer to my understanding) that includes everything EXCEPT the corpus callosum and the unknown. However, I summed all the surface areas and took and average of all the thickness measurements and they are very close to the values printed at the top of the sheet. Another observation I had made was that the total surface area measurement has a decimal and the surface area for the ROIs appears to be rounded and if they were not rounded the values would be the same. For the thickness values, the value I calculated and the one on the sheet are within the average of the standard deviation each other. > > > If my understanding is incorrect please let me know and provide insight into how we may calculate these global measurements correctly. > > > Thank you in advance for your time, > > Tara Palin > > > ---------------------------------------------------------------------- > Disclaimer: > > > The materials in this e-mail are private and may contain Protected Information. Please note that e-mail communication is not encrypted by default. You have the right to request further emails be encrypted by notifying the sender. Your continued use of e-mail constitutes your acknowledgment of these confidentiality and security limitations. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution, or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this e-mail in error, please immediately notify the sender via telephone or return e-mail. >

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mri_volsynth question
by Nasiriavanaki, Zahra 10 Sep '20

10 Sep '20

Hi I am trying to make a subcortical 5 mm sphere ROI around a talairach coordinate. I am using the below command, but when I visualize it, it doesn’t look at the correct location. I see the same question in forum (https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg67295.html) I should probably use -pdf delta but I don’t know how to get the col, row and slice indices of the vertex where it should go. mri_volsynth --template $SUBJECTS_DIR/fsaverage/mri/brainmask.mgz --c_ras -21.8 -12.2 -10.3 --dim 5 5 5 5 —o new.mgh I appreciate your help. Thanks Mona Zahra (Mona) Nasiriavanaki, M.D. Postdoctoral Research Fellow Department of Psychiatry Massachusetts General Hospital 149 13th Street, 149-2615 Charlestown, MA, USA, 02129

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FLAIR to improve pial segmentation? What are the surfaces used for stat estimation?
by Otília C. d'Almeida 10 Sep '20

10 Sep '20

External Email - Use Caution Hi FS community, I started using FS 7.1.0 for cortical and subcortical parcellation/segmentation. As I found information that FLAIR data could improve pial surfaces creation, I decided to try it on since I have FLAIR images besides MPRAGE, by using the command line form FSwiki: RECON-ALL -SUBJECT NAME -I INPUT_VOLUME.NII -FLAIR FLAIR_VOLUME.NII -FLAIRPIAL -ALL However when I opened Freeview, I overlaid RH.PIAL, and RH.PIAL.FLAIR, RH.PIAL.T1. The first two are quite similar (overlap) and the segmentation is worse than rh.pial.T1. So, my question is, what is really the final surface of recon-all that must be checked for errors and that is used for stats estimation? Thank you in advance. Best regards, Otília

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Freesurfer September 2020