Freesurfer December 2016

freesurfer@nmr.mgh.harvard.edu

95 participants
146 discussions

(no subject)
by Sadhana Singh 16 Dec '16

16 Dec '16

Hello FreeSurfer Developers, I'm running the recon-all on my subjects data as described in freesurfer tutorial (https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial) but it shows the following error when I run the recon-all command: ERROR: cannot find CON_101.nii recon-all -s exited with ERRORS I've tried so many times but still shows same errors. 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: Red Hat Enterprise Linux 7 3) uname -a: Linux lcmodel 3.10.0-327.el7.x86_64 #1 SMP Thu Oct 29 17:29:29 EDT 2015 x86_64 x86_64 x86_64 GNU/Linux 4) recon-all.log: see attached Regards *Sadhana Singh, PhD * *Postdoctoral Researcher* *Departments of Anesthesiology * *David Geffen School of Medicine at UCLA * *University of California at Los Angeles * *Los Angeles, CA, USA* *Phone No: 424-270-4940 * *Email: sadhanasingh(a)mednet.ucla.edu <sadhanasingh(a)mednet.ucla.edu> *

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Re: [Freesurfer] V6 FS eTICV versus CAT12 TICV with Small Heads
by Harms, Michael 16 Dec '16

16 Dec '16

Wow, that’s a terrible correlation between two putative measures of head size. What does the scatterplot of FS’s “eTIV” vs “SupraTentorialVol” look like? The latter is based on the surfaces, so a scatterplot of the two can be a good way to identify cases where the talairach.xfm file (from which “eTIV” is derived) isn’t very accurate. cheers, -MH -- Michael Harms, Ph.D. ----------------------------------------------------------- Conte Center for the Neuroscience of Mental Disorders Washington University School of Medicine Department of Psychiatry, Box 8134 660 South Euclid Ave. Tel: 314-747-6173 St. Louis, MO 63110 Email: mharms(a)wustl.edu From: <freesurfer-bounces(a)nmr.mgh.harvard.edu<mailto:freesurfer-bounces@nmr.mgh.harvard.edu>> on behalf of Jeffrey Crawford <jcrawf29(a)jhmi.edu<mailto:jcrawf29@jhmi.edu>> Reply-To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> Date: Friday, December 16, 2016 at 11:56 AM To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> Subject: [Freesurfer] V6 FS eTICV versus CAT12 TICV with Small Heads Hello everyone! I have some questions about FS eTICV. I read on the Wiki that eTICV is not the best measure of ICV and saw the same from other articles. The alternative I decided on was measuring the TICV using CAT12 from SPM. I decided to do a scatterplot of the eTICV from FS V6 and TICV from CAT12 to see how they match each other on measurment. FS is the variable on the Y-axis and CAT12 is the variable on the X-axis. If we assume that CAT12 is more accurate than FS, then it looks as though the FS begins to become more inaccurate as the head size gets smaller. [cid:image001.png@01D2579B.8A615E30] So here are my questions: 1. Is my interpretation of this scatterplot correct? 2. Does FS generally have more difficulty measuring smaller heads? If so, then why? 3. Is it more advised for me to use the CAT12 TICV measure as a covariate in my future analysis? Or maybe some other program that I don’t know about? ________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.

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ERROR: the pixel data cannot be loaded as it is JPEG compressed.
by Warner, Graham Cary 16 Dec '16

16 Dec '16

Hi, I'm trying to open a dicom using the center's instillation of freesurfer (/usr/local/freesurfer/nmr-stable53-env) but get the following error message when trying to load the file. Starting DICOMRead2() dcmfile = /autofs/space/jazz_001/users/gwarner/mi2b2Data/1.2.124.113532.132.183.36.32.20040903.132017.11895667/1.2.840.113619.2.25.49466.102.1094369499/1.2.840.113619.2.25.49466.102.1.1094369499.dcm dcmdir = /autofs/space/jazz_001/users/gwarner/mi2b2Data/1.2.124.113532.132.183.36.32.20040903.132017.11895667/1.2.840.113619.2.25.49466.102.1094369499 Ref Series No = 102 Found 25 files, checking for dicoms Found 23 dicom files in series. First Sorting Computing Slice Direction Vs: 0 0 6 Vs: 0 0 1 Second Sorting Counting frames nframes = 1 nslices = 23 ndcmfiles = 23 PE Dir = COL (dicom read) TransferSyntaxUID: --1.2.840.10008.1.2.4.70-- ERROR: the pixel data cannot be loaded as it is JPEG compressed. (Transfer Syntax UID: 1.2.840.10008.1.2.4.70) jpegUID: --1.2.840.10008.1.2.4-- I am able to open the file in pydicom and even view the binary of the pixel data but crash again when I try to use the pixel_array function. The pydicom error also indicates that it can't handle the JSON compression. It looks like I'm not the first person to have this problem (https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg40683.html) but the solution given here won't work for me because I can't write to the directory mentioned. Does anyone know another way to solve this? Thank you, Graham

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Re: [Freesurfer] License problem
by Marco Ganzetti 16 Dec '16

16 Dec '16

At the current stage I can run recon-all and get the results without problems. If the license would not work I couldn't be able to run it. Can someone send me the type of license file I should generate? In the website it says that I should get a license.txt by email, but I didn't get any file just instructions how to create a new file or modify the existing LICENSE file. Marco Ganzetti, PhD Il 16 Dic 2016 19:47, Z K <zkaufman(a)nmr.mgh.harvard.edu> ha scritto: Is the file you created located in /Applications/freesurfer? Also, fir good measure, try creating the same file but naming it .license in the /Applications/freesurfer On 12/16/2016 11:20 AM, Marco Ganzetti wrote: > Dear all, > I am trying to display a volumetric file to a surface using mri_vol2surf > and then tksurfer. > Here is the error message I get. > > I have obtained the email with the few license lines to copy in a file > (that i created) name license.txt > I created a new file and erased the existing LICENSE > > Thanks > Marco Ganzetti > > Last login: Fri Dec 16 16:56:54 on ttys002 > -------- freesurfer-Darwin-lion-stable-pub-v5.3.0 -------- > Setting up environment for FreeSurfer/FS-FAST (and FSL) > FREESURFER_HOME /Applications/freesurfer > FSFAST_HOME /Applications/freesurfer/fsfast > FSF_OUTPUT_FORMAT nii.gz > SUBJECTS_DIR /Applications/freesurfer/subjects > MNI_DIR /Applications/freesurfer/mni > FSL_DIR /usr/local/fsl > Binds-MacBook-Pro:~ Marco$ source ~/.bash_profile > -------- freesurfer-Darwin-lion-stable-pub-v5.3.0 -------- > Setting up environment for FreeSurfer/FS-FAST (and FSL) > FREESURFER_HOME /Applications/freesurfer > FSFAST_HOME /Applications/freesurfer/fsfast > FSF_OUTPUT_FORMAT nii.gz > SUBJECTS_DIR /Applications/freesurfer/subjects > MNI_DIR /Applications/freesurfer/mni > FSL_DIR /usr/local/fsl > Binds-MacBook-Pro:~ Marco$ export > SUBJECTS_DIR=/Users/Marco/Desktop/surface_RORDEN > Binds-MacBook-Pro:~ Marco$ mri_vol2surf --src > /Users/Marco/Desktop/surface_RORDEN/GM_SPM12_OneSampT_tstat1.nii > --regheader elab --hemi lh --o > /Users/Marco/Desktop/surface_RORDEN/GM_SPM12_OneSampT_tstat1_SURF_LH.mgh > srcvol = /Users/Marco/Desktop/surface_RORDEN/GM_SPM12_OneSampT_tstat1.nii > srcreg unspecified > srcregold = 0 > srcwarp unspecified > surf = white > hemi = lh > reshape = 0 > interp = nearest > float2int = round > GetProjMax = 0 > INFO: float2int code = 0 > Done loading volume > Computing registration from header. > Using /Users/Marco/Desktop/surface_RORDEN/elab/mri/orig.mgz as target > reference. > Reading surface /Users/Marco/Desktop/surface_RORDEN/elab/surf/lh.white > Done reading source surface > Mapping Source Volume onto Source Subject Surface > 1 0 0 0 > using old > Done mapping volume to surface > Number of source voxels hit = 41923 > Writing to > /Users/Marco/Desktop/surface_RORDEN/GM_SPM12_OneSampT_tstat1_SURF_LH.mgh > Dim: 116772 1 1 > Binds-MacBook-Pro:~ Marco$ tksurfer elab lh inflated -overlay > /Users/Marco/Desktop/surface_RORDEN/GM_SPM12_OneSampT_tstat1_SURF_LH.mgh > subject is elab > hemi is lh > surface is inflated > surfer: current subjects dir: /Users/Marco/Desktop/surface_RORDEN > surfer: not in "scripts" dir ==> using cwd for session root > surfer: session root data dir ($session) set to: > surfer: /Users/Marco > checking for nofix files in 'inflated' > Reading image info (/Users/Marco/Desktop/surface_RORDEN/elab) > Reading /Users/Marco/Desktop/surface_RORDEN/elab/mri/orig.mgz > surfer: Reading header info from > /Users/Marco/Desktop/surface_RORDEN/elab/mri/orig.mgz > -------------------------------------------------------------------------- > ERROR: FreeSurfer license file /Applications/freesurfer/.license not found. > If you are outside the NMR-Martinos Center, > go to http://surfer.nmr.mgh.harvard.edu to > get a valid license file (it's free). > If you are inside the NMR-Martinos Center, > make sure to source the standard environment. > -------------------------------------------------------------------------- > Binds-MacBook-Pro:~ Marco$ > > - - - > > *Marco Ganzetti, PhD* > > Movement Control & Neuroplasticity Research Group > Tervuursevest 101, 3001 Leuven > > email: marco.ganzetti(a)kuleuven.be <mailto:marco.ganzetti@kuleuven.be> > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.

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(no subject)
by Sadhana Singh 16 Dec '16

16 Dec '16

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License problem
by Marco Ganzetti 16 Dec '16

16 Dec '16

Dear all, I am trying to display a volumetric file to a surface using mri_vol2surf and then tksurfer. Here is the error message I get. I have obtained the email with the few license lines to copy in a file (that i created) name license.txt I created a new file and erased the existing LICENSE Thanks Marco Ganzetti Last login: Fri Dec 16 16:56:54 on ttys002 -------- freesurfer-Darwin-lion-stable-pub-v5.3.0 -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /Applications/freesurfer FSFAST_HOME /Applications/freesurfer/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /Applications/freesurfer/subjects MNI_DIR /Applications/freesurfer/mni FSL_DIR /usr/local/fsl Binds-MacBook-Pro:~ Marco$ source ~/.bash_profile -------- freesurfer-Darwin-lion-stable-pub-v5.3.0 -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /Applications/freesurfer FSFAST_HOME /Applications/freesurfer/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /Applications/freesurfer/subjects MNI_DIR /Applications/freesurfer/mni FSL_DIR /usr/local/fsl Binds-MacBook-Pro:~ Marco$ export SUBJECTS_DIR=/Users/Marco/Desktop/surface_RORDEN Binds-MacBook-Pro:~ Marco$ mri_vol2surf --src /Users/Marco/Desktop/surface_RORDEN/GM_SPM12_OneSampT_tstat1.nii --regheader elab --hemi lh --o /Users/Marco/Desktop/surface_RORDEN/GM_SPM12_OneSampT_tstat1_SURF_LH.mgh srcvol = /Users/Marco/Desktop/surface_RORDEN/GM_SPM12_OneSampT_tstat1.nii srcreg unspecified srcregold = 0 srcwarp unspecified surf = white hemi = lh reshape = 0 interp = nearest float2int = round GetProjMax = 0 INFO: float2int code = 0 Done loading volume Computing registration from header. Using /Users/Marco/Desktop/surface_RORDEN/elab/mri/orig.mgz as target reference. Reading surface /Users/Marco/Desktop/surface_RORDEN/elab/surf/lh.white Done reading source surface Mapping Source Volume onto Source Subject Surface 1 0 0 0 using old Done mapping volume to surface Number of source voxels hit = 41923 Writing to /Users/Marco/Desktop/surface_RORDEN/GM_SPM12_OneSampT_tstat1_SURF_LH.mgh Dim: 116772 1 1 Binds-MacBook-Pro:~ Marco$ tksurfer elab lh inflated -overlay /Users/Marco/Desktop/surface_RORDEN/GM_SPM12_OneSampT_tstat1_SURF_LH.mgh subject is elab hemi is lh surface is inflated surfer: current subjects dir: /Users/Marco/Desktop/surface_RORDEN surfer: not in "scripts" dir ==> using cwd for session root surfer: session root data dir ($session) set to: surfer: /Users/Marco checking for nofix files in 'inflated' Reading image info (/Users/Marco/Desktop/surface_RORDEN/elab) Reading /Users/Marco/Desktop/surface_RORDEN/elab/mri/orig.mgz surfer: Reading header info from /Users/Marco/Desktop/surface_RORDEN/elab/mri/orig.mgz -------------------------------------------------------------------------- ERROR: FreeSurfer license file /Applications/freesurfer/.license not found. If you are outside the NMR-Martinos Center, go to http://surfer.nmr.mgh.harvard.edu to get a valid license file (it's free). If you are inside the NMR-Martinos Center, make sure to source the standard environment. -------------------------------------------------------------------------- Binds-MacBook-Pro:~ Marco$ - - - Marco Ganzetti, PhD Movement Control & Neuroplasticity Research Group Tervuursevest 101, 3001 Leuven email: marco.ganzetti(a)kuleuven.be<mailto:marco.ganzetti@kuleuven.be>

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V6 FS eTICV versus CAT12 TICV with Small Heads
by Jeffrey Crawford 16 Dec '16

16 Dec '16

Hello everyone! I have some questions about FS eTICV. I read on the Wiki that eTICV is not the best measure of ICV and saw the same from other articles. The alternative I decided on was measuring the TICV using CAT12 from SPM. I decided to do a scatterplot of the eTICV from FS V6 and TICV from CAT12 to see how they match each other on measurment. FS is the variable on the Y-axis and CAT12 is the variable on the X-axis. If we assume that CAT12 is more accurate than FS, then it looks as though the FS begins to become more inaccurate as the head size gets smaller. [cid:image001.png@01D2579B.8A615E30] So here are my questions: 1. Is my interpretation of this scatterplot correct? 2. Does FS generally have more difficulty measuring smaller heads? If so, then why? 3. Is it more advised for me to use the CAT12 TICV measure as a covariate in my future analysis? Or maybe some other program that I don't know about?

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FLAIR T1 misregistration
by Robert Kraft 16 Dec '16

16 Dec '16

I am trying to run recon-all with a T1w image and a FLAIR image to improve the removal of the dura. I am using the command recon-all -sd /cenc/mri/freesurfer -subjid 34P1001 -all -i /cenc/mri/subjects/34P1001/freesurfer/input/t1w.nii.gz -FLAIR /cenc/mri/subjects/34P1001/freesurfer/input/t2flair.nii.gz -FLAIRpial I have two questions. First, in reading the forums I read several threads on the forum saying that you run the recon-all without the -FLAIRpial option and then run recon-all -autorecon3 -s $SUBJECT -FLAIRpial — (http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg28033.html) Is it necessary to run -autorecon3 with -FLAIRpial option after recon-all has been run with the T1w image? It seems that if the -FLAIRpial option only is needed in -autorecon3 then it should be able to be specified simultaneously. I did try it the way posted with similar results for some images. My biggest concern is that there is a severe misregistration between my T1w image and my FLAIR image. What can I do to improve the registration? The raw data are almost perfectly aligned (i.e. the subject did not move between acquisitions) so this misregistration has me baffled.. After registration the FLAIR image has been shifted and rotated. There is also a hyper intensity shading on the superior brain regions (best seen in the sagittal view). I have posted the mri and scripts folder to Google Drive if anyone cares to take a look https://drive.google.com/drive/folders/0B4bmIh8K5WVJbDRpNXh1TVEzdVU?usp=sha… I have also included 3 screen shots showing the issue of misregistration and hyper intensities. Any suggestions on how to resolve this issue would be greatly appreciated. Thanks for your help in advance Bob

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Re: [Freesurfer] how to make label from volumetric mask? (Douglas N Greve)
by Niia Nikolova 16 Dec '16

16 Dec '16

Thank you, that worked perfectly!

1 0

6.0 release date?
by Vaz pandolfo, Renata 16 Dec '16

16 Dec '16

Dear FS experts, My colleagues and I are planning some projects and we were wondering if there are any news on the release date of the FreeSurfer 6.0 stable version. We noticed that there was a new developmental version released today, is that good news? An approximation of whether it will be a matter of weeks or months would suffice. Thank you! Renata

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Freesurfer December 2016