Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30076 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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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?

1 0

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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questions about registration tool in Freesurfer
by Frank Robert 15 Dec '16

15 Dec '16

Dear FS experts I want to use Freesurfer registration tools. I check https://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferCommandsRegistration?hi… 1). Here it is the term " modality" I want to get clarification. It is easy to know Modality is different between CT, MRI and PET. But if MRI use different sequence, T1, T2, DWI, ASL to get different images, it is the same modality or different modality? 2). mri_coreg is strongly recommended for use. But I can not find the instruction in Wiki. 3.) If I register ASL source image and subtraction images to T1w images, I guess that preciseness of registration will be higher if use source images to register. Is it right? If it is correct, If I use ASL source images to register to get .lta file, how can I apply .lta file to apply for subtraction images? Do you have instruction? Many thanks Best Regards Frank Yu

1 0

(no subject)
by Sadhana Singh 15 Dec '16

15 Dec '16

Hi I am using freesurfer for calculation cortical thickness in my subjects. Firstly, I have converted all the T1 weighted images from dcm into nii.gz format. After that, I have run the recon-all in one subject using this script 'recon-all -i CON_101.nii -s CON_101 -all' , but it shows error The error is: [kumarlab@lcmodel ~]$ cd /home/kumarlab/Downloads/ Freesurfer_VBM [kumarlab@lcmodel Freesurfer_VBM]$ export SUBJECTS_DIR=/home/kumarlab/ Downloads/Freesurfer_VBM [kumarlab@lcmodel Freesurfer_VBM]$ recon-all -i CON_101.nii -s CON_101 -all ERROR: cannot find CON_101.nii 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 recon-all -s exited with ERRORS at Thu Dec 15 16:14:29 EST 2016 Regards *Sadhana Singh, PhD *

3 2

mri_coreg question
by Frank Robert 15 Dec '16

15 Dec '16

Hello FS experts I followed the instruction to download the mri_coreg file from website https://gate.nmr.mgh.harvard.edu/safelinks/greve/mri_coreg put it on my virtual machine ubuntu \local\user\freesurfer\bin directory. But I run it and it say <https://gate.nmr.mgh.harvard.edu/safelinks/greve/mri_coreg> \local\user\freesurfer\bin\mri_coreg can not execute binary file? I use sudo chmod u+x mri_coreg to make it executable. Do you know why? Frank Yu Douglas N Greve <greve(a)nmr.mgh.harvard.edu> Oct 3 to freesurfer you can get it from here https://gate.nmr.mgh.harvard.edu/safelinks/greve/mri_coreg On 10/03/2016 12:46 PM, Hsin-Tsung Lee wrote: > Dear Dr. Bruce > I have one more question, does the "mri_coreg" available in > version 5.30 stable, or it only available in v6.0(or it's beta version)? > > Best Regard

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Infant brain atlas
by Axelson, Eric D 15 Dec '16

15 Dec '16

I asked this last week with no response: Does the infant brain atlas mentioned in this paper https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4332305/ exist yet or will it be included in version 6? Thanks Eric Axelson Research Specialist Department of Psychiatry University of Iowa eric-axelson(a)uiowa.edu<mailto:eric-axelson@uiowa.edu> ________________________________ Notice: This UI Health Care e-mail (including attachments) is covered by the Electronic Communications Privacy Act, 18 U.S.C. 2510-2521 and is intended only for the use of the individual or entity to which it is addressed, and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If you are not the intended recipient, any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please notify the sender immediately and delete or destroy all copies of the original message and attachments thereto. Email sent to or from UI Health Care may be retained as required by law or regulation. Thank you. ________________________________

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