Freesurfer

freesurfer@nmr.mgh.harvard.edu

21 participants
30071 discussions

FS 6.0 Freeview
by Daniel Carey 23 Feb '17

23 Feb '17

Dear All, I've recently installed FS 6.0 on Mac (OS 10.7.5), and have been unable to load volumes in Freeview. When selecting 'File > Load volume', the dialog box appears, but when I select any T1.mgz and click Ok, Freeview immediately crashes. Has anyone encountered this same issue? Best wishes, Dan --- Dr. Daniel Carey Post-Doctoral Research Fellow - Statistician The Irish LongituDinal Study on Ageing (TILDA) Trinity College Dublin Dublin 2, Ireland. Email: careyda(a)tcd.ie

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Re-running after Base Image Edits
by Corrina Fonseca 22 Feb '17

22 Feb '17

Hi there, We are attempting edits on base images and a couple of questions came up when re-running through the pipeline: 1. After cp, wm, or pial edits on the base image, is it okay to simply start at ‘-autorecon2’ or must the specific starting points be used? (ie. “-autorecon2-cp”, “-autorecon2-wm”, “-autorecon2-pial”). 2. When re-running a base, after edits, starting at autorecon2, is it necessary to include all the timepoints in the command like (ie. “-tp subj1 –tp subj2”)? It’d make things simpler if that wasn’t necessary and our reading of the longitudinal processing protocol seems to suggest all the “tp” related stuff happens in autorecon1 when the norm image and transformations are generated. After that, the doc suggests that it simply processes that averaged image per-usual. Thanks in advance for any help! *Corrina Fonseca* Staff Research Associate II Senior Imaging Technician *Center for Imaging of Neurodegenerative Diseases* *San Francisco VA Medical Center* *4150 Clement Street (114M)* *San Francisco, CA 94121* *http://www.radiology.ucsf.edu/cind <http://www.radiology.ucsf.edu/cind>* *(415) 221-4810 x23088*

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gzip: stdin: unexpected end of file
by Kambiz Tavabi 22 Feb '17

22 Feb '17

After downloading CentOS 6 x86_64 (64b) stable v6.0.0 unzipping on Ubunt 16.04 (64b) machine with tar -C /usr/local -xzvf freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0.tar.gz Returns an error: gzip: stdin: unexpected end of file tar: Child returned status 1 tar: Error is not recoverable: exiting now Is there a way around this? ------------------------------------------------------------ Kambiz Tavabi PhD Institute for Learning & Brain Sciences 1715 Columbia Road N Portage Bay Building Box 357988 University of Washington Seattle, WA 98195-7988 Tel: 206-685-6173 ------------------------------------------------------------ *Confidentiality Notice: Because email is not secure, please be aware that we cannot guarantee the confidentiality of information sent by email. If you are not the intended recipient of this email, please notify the sender by reply email, and then destroy all copies of the message and any attachments.*

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No FTP Access
by Rockers, Elijah D. 22 Feb '17

22 Feb '17

Is there by any chance another way to download Freesurfer? My institution does not allow FTP connections (HIPPA...) Same goes for the tutorial data, but obviously Freesurfer is the priority here... thanks. - Eli Houston Methodist. Leading Medicine. U.S. News & World Report has recognized Houston Methodist as one of the nation’s top 20 hospitals, placing it for the second time on the magazine’s prestigious Honor Roll. It is also designated as a Magnet hospital for excellence in nursing. Visit us at houstonmethodist.org. Follow us at twitter.com/MethodistHosp and www.facebook.com/HoustonMethodist. ***CONFIDENTIALITY NOTICE*** This e-mail is the property of Houston Methodist Hospital and/or its relevant affiliates and may contain restricted and privileged material for the sole use of the intended recipient(s). Any review, use, distribution or disclosure by others is strictly prohibited. If you are not the intended recipient (or authorized to receive for the recipient), please contact the sender and delete all copies of the message. Thank you.

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Accessing Freesurfer
by Ly, Kien-Ninh Ina,M.D. 22 Feb '17

22 Feb '17

Hi, I’m trying to access Freesurfer on my Mac but have been unable to do so. It appears that I’m sourcing Freesurfer through nmr-stable6-env but an error message keeps showing up when I type in “freeview”. I’ve also tried doing the Freesurfer tutorials online but the same error message appears. Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /usr/local/freesurfer/stable6 FSFAST_HOME /usr/local/freesurfer/stable6/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /space/sake/3/users/inverse/subjects MNI_DIR /usr/local/freesurfer/stable6/mni FSL_DIR /usr/pubsw/packages/fsl/current [scheherazade:~] (nmr-stable6-env) freeview X Error: BadValue (integer parameter out of range for operation) 2 Extension: 149 (Uknown extension) Minor opcode: 3 (Unknown request) Resource id: 0x0 Abort (core dumped) Any thoughts on how to fix this? Many thanks, Ina

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mri_nu_correct.mni error after manual talairach alignment
by teodora petrova 22 Feb '17

22 Feb '17

Hello Freesurfer Developers, I have tried a manual Talairach alignment, according to this tutorial: http://freesurfer.net/fswiki/FsTutorial/Talairach_freeview . But when I run the command recon-all -all -subjid 42dd63ba-7ad6-4098-9335-6ecebc46dd41 , the run stops at the following step: #-------------------------------------------- #@# Talairach tor 16 feb 2017 11:09:05 CET /data-02/teodora/FreeSurfer/42dd63ba-7ad6-4098-9335-6ecebc46dd41/mri mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale --i orig.mgz --o orig_nu.mgz Linux siv 4.4.0-62-generic #83-Ubuntu SMP Wed Jan 18 14:10:15 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux recon-all -s 42dd63ba-7ad6-4098-9335-6ecebc46dd41 exited with ERRORS at tor 16 feb 2017 11:09:08 CET I have searched in the support archives, but I did not find a complete solution of the problem in none of the threads. 1) FreeSurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 2) Platform: Ubuntu MATE 16.04 3) see recon-all.log attached Thank you for your help. Best,Teodora

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Neonatal Cortical thickness from T2 weight MRI
by Flavia Arduini 22 Feb '17

22 Feb '17

Hi, I'm doing a research work for the 'Bambino Gesù' Hospital in Rome. I segmented with Mantis MRI T2-weighted of infants. Now I have to estimate the cortical thickness and I want to do it with FREESURFER. There is a script extrapolated from segmentation relating only to the cortical thickness? I thank you in advance Regards

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Post-doc proposal: Charting the human brain with fMRI
by Ana Luísa Pinho 22 Feb '17

22 Feb '17

Please find enclosed a post-doc proposal for an original "exhaustive cognitive mapping" performed in the framework of the Human Brain Project. *Duration & salary*: 12 months renewable up to 3 years, about 2100 enet monthly *Research teams*: Parietal (INRIA Saclay) and Unicog (INSERM), located at Neurospin, Saclay,France. *Responsible:* Bertrand Thirion. Contact: bertrand.thirion(a)inria.fr *Application*: Interested candidate should send CV and motivation letter. The post-doc will be in charge of setting a set of protocols up and running to pass them on the existing pool of 12 subjects of the Individual Brain Charting project. These protocols will be provided by the community (potentially from in-house developments) are meant to cover a large array of sensory, motor and cognitive processes. The post-doc will take part to the set of acquisitions performed on Neurospin 3T scanner at high resolution (1.5mm) and analyze the data by using a pipeline provided by the lab. Detailed reports will be provided to assess the quality of the data, motivate the participants and document the content of the database. These reports will provide extensive information on the functional organization of the brain in each individual, which will furthermore be confronted to other imaging modalities, e.g. anatomical and functional connectivity. Complex alignment procedures will then be carried out to obtain a population-level mapping that will lead to the first data-based cognitive atlas of the human brain. The data and atlas and analysis material will be released publicly. See https://team.inria.fr/parietal/files/2011/07/post-doc_ibc-1.pdf for details.

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Manual hippocampal segmentation
by Michel Hu 22 Feb '17

22 Feb '17

Dear freesurfer experts, I was wondering if it's possible to manually segment the dentate gyrus on a 3T scan? If so are there any resources you could point me too? Thank you for your time. Sincerely, Mike Zhou

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Re: [Freesurfer] Convolving external regressors with HRF
by Reza Rajimehr 22 Feb '17

22 Feb '17

Thank you so much Doug! I just have one more question: Before convolving regressors with HRF, I looked at X matrix and noticed that the values of regressors have been changed/scaled. For example, the original values in a regressor file are: 134.8300 0 141.1200 0 91.5310 0 96.1870 0 But they have been apparently shifted by a constant value in the X matrix: 91.8168 -43.0132 98.1068 -43.0132 48.5178 -43.0132 53.1738 -43.0132 Why is there such a change in the regressor values? Thanks, Reza You can use the following matlab code. You can ignore the warning printed after the toepliz operation. The OriginalRegressor should be a vector of length Ntp, then write out the NewRegressor to a new external regressor file. TR=2; % seconds Ntp=100; t = TR*[0:Ntp-1]'; h = fast_spmhrf(t); a = zeros(Ntp,1); a(1) = 1; X = toeplitz(h,a); NewRegressor = X*OriginalRegressor; On 02/21/2017 04:02 PM, Reza Rajimehr wrote: >* Hi Doug, *>>* Since our external regressors are stimulus-related (e.g. mean *>* luminance of stimuli), we need to convolve them with a hemodynamic *>* response function. In mkanalysis-sess, we have used -spmhrf 0 to model *>* conditions. Is there a code or Matlab script for HRF convolution, so *>* that we apply exactly the same spmhrf function for modeling the *>* external regressors? *>>* Thanks, *>* Reza *>>* No, they are not *>>>* On 02/17/2017 05:09 PM, Reza Rajimehr wrote: *>* >/During the functional analysis in FS-FAST, are the external regressors />/convolved with the hemodynamic response function? />//>/Thanks, />/Reza />//>//>/_______________________________________________ />/Freesurfer mailing list />/Freesurfer at nmr.mgh.harvard.edu <http://nmr.mgh.harvard.edu> *>* <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>> />/https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> / *>* -- *>* Douglas N. Greve, Ph.D. *>* MGH-NMR Center *>* greve at nmr.mgh.harvard.edu <http://nmr.mgh.harvard.edu> *>* <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>> *>* Phone Number: 617-724-2358 *>* Fax: 617-726-7422 *>>* Bugs:surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> *>* <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>> *>* FileDrop:https://gate.nmr.mgh.harvard.edu/filedrop2 <https://gate.nmr.mgh.harvard.edu/filedrop2> *>* www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> *>* <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>> *>* Outgoing:ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/> *>>>* _______________________________________________ *>* Freesurfer mailing list *>* Freesurfer at nmr.mgh.harvard.edu <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> *>* https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> * -- Douglas N. Greve, Ph.D. MGH-NMR Centergreve at nmr.mgh.harvard.edu <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2www.nmr.mgh.harvard.edu/facility/… Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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