Freesurfer February 2017

freesurfer@nmr.mgh.harvard.edu

162 participants
277 discussions

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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Does recon-all conduct cortical parcellation on the nu.mgz?
by Lee Subin Kristine 22 Feb '17

22 Feb '17

Dear FreeSurfer, Hello, I have been using the preprocessed images (which have already undergone N3 correction) from the Alzheimer's Disease Neuroimaging Initiative database as input for recon-all -all.( version 5.3.1) I have 3 questions: (1) Does recon-all use the nu.mgz during subcortical segmentation and cortical parcellation? (2) If so, then would my image be effectively undergoing N3 "twice", and does this affect the accuracy of the segmentation in any way? (3) A bit of a side question, but does rescaling to isovoxels and performing ACPC aligment before recon-all make the segmentation results more accurate? Thank you in advance. Best regards, Kristine

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Freeview
by N Saf 22 Feb '17

22 Feb '17

Dear Experts, I load the T1 and aseg file in freeveiw and select the lookup table ,and show as isosurface in 3D view for a label .Is it possible to change the color(for example label 13 is blue but I want to show it as yellow!).another question is that if I want to show multiple labels which are not in the range how should I do it ? for example I want to see labels 11 & 13 & 30 but not the lables between ,how can I do it?thanks for your support. Best Regards, Nazanin

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Re: [Freesurfer] -trac-all -prep FS 5.3 Memory Allocation Issue
by Yendiki, Anastasia 21 Feb '17

21 Feb '17

Hi Abby – When you say you have successfully processed a subject on that machine before, what FS version was that with? What has changed since then? The last I remember memory allocation issues, they were years ago in a very old version of OSX that we don’t even distribute binaries for any more, so I don’t think this is the same problem. Best, a.y From: <freesurfer-bounces(a)nmr.mgh.harvard.edu<mailto:freesurfer-bounces@nmr.mgh.harvard.edu>> on behalf of Abigail Waters <awaters2(a)suffolk.edu<mailto:awaters2@suffolk.edu>> Reply-To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> Date: Friday, February 10, 2017 at 3:05 PM 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] -trac-all -prep FS 5.3 Memory Allocation Issue Hello - I'm attempting to run the -trac-all -prep command with FS 5.3. I am running into the same memory allocation issues on my Mac that were present in earlier versions of Freesurfer/Tracula. See below: MRIallocSequence (218, 182, 1):could not allocate 158784 bytes for the 44th slice Cannot allocate memory I have attempted the pre-processing with multiple and single subjects. I have successfully processed a single subject on this machine before, and have not updated to the latest Freesurfer since that subject (as all MPRAGE scans were reconstructed is FS 5.3). There is sufficient memory available and the MPRAGE scans were reconstructed correctly. Any thoughts on how to solve the issue would be appreciated. Please let me know if you need any additional information. Thanks! Abby

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contrast matrix for one-way ANOVA with 1 factor, 4 groups
by Gold, Andrea (NIH/NIMH) [F] 21 Feb '17

21 Feb '17

Hi, I am trying to run a cortical thickness analysis comparing four groups – my goal is to conduct an omnibus F-test testing for any group differences. I have 0 covariates/nuisance regressors. This would be equivalent to the “Contrast 4 group.effect.mtx” in this page, for 3 groups: https://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf3G0V But, instead of 3 groups I have 4 groups. I thought the contrast matrix for 4 groups F-test would be: 1 -1 0 0 0 1 -1 0 0 0 1 -1 But for 3 groups it is: 1 -1 0 1 0 -1 Would you please clarify the correct contrast matrix for this test in Freesurfer mri_glmfit? Thank you! Andrea -- Andrea Gold, Ph.D. Section on Development and Affective Neuroscience National Institute of Mental Health 9000 Rockville Pike MSC 2670 Bldg. 15K Bethesda, MD 20892 Phone: 301-402-6955 Fax: 301-402-2010 Email: andrea.gold(a)nih.gov

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Cerebral (without ventricles) Volume = aseg.stats / SupraTentorialNotVent ?
by Kaiming Yin 21 Feb '17

21 Feb '17

Dear guys, Could I ask which value in the stats/aseg.stats represents the volume of the cerebrum (including the subcortical structures while excluding the ventricles and brain stem)? I'm not sure whether the "SupraTentorialNotVent" can be the value for this measurement, and could it be a bit bigger than the real value due to the partial volume effect? Besides, could I also ask is there a value represent the volume of the cerebellum? Currently I calculate the volume by adding the left/right cerebellar GM/WM values in the detailed list in aseg.stats file. Many thanks, Kaiming

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cannot "git pull" from freeSurfer git repository
by Antonin Skoch 21 Feb '17

21 Feb '17

Dear experts, I am recently not able to pull from freeSurfer git repository. The error message is following: error: The requested URL returned error: 403 Forbidden (curl_result = 22, http_code = 403, sha1 = b3b71d49c42db73a6f1dad0229111dc3f900a1d3) error: Unable to find b3b71d49c42db73a6f1dad0229111dc3f900a1d3 under https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/repo/freesurfer.git Cannot obtain needed object b3b71d49c42db73a6f1dad0229111dc3f900a1d3 error: fetch failed. Git clone to the fresh empty directory exits with similar error. Did you recently forbid access to freeSurfer git repository to external users? Regards, Antonin Skoch

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Freesurfer February 2017