Freesurfer

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30096 discussions

Re: [Freesurfer] Re Re Re Re: Question regarding mri_convert
by Tamara Tavares 29 Sep '16

29 Sep '16

I looked at some structures and the absolute differences range from 8-35 mm^3. They are quite small but I was surprised to see any difference since they are the same scan. Thanks, Tamara Hi Tamara can you let us know how big the differences are? thanks Bruce On Wed, 28 Sep 2016, Douglas Greve wrote: > > I don't understand what the problem is. Can you elaborate? > > > On 9/27/16 12:13 PM, Tamara Tavares wrote: > The differences have been found in the outputs from the aseg > file. Particularly, I am interested in the ventricles and the > intracranial volumes. I have loaded both anatomicals in FreeView > and toggled between them and have found no differences visually. > ? > > I have attached the files (Via Google Drive since they are large). > They are from the same participant. > > Thank you again, > Tamara > > ?[icon_10_generic_list.png] ?rawavg_MriConvert.mgz[x_8px.png] > ??[icon_10_generic_list.png] ?rawavgSlicer4.mgz[x_8px.png] > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >

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Re: [Freesurfer] REPOST cluster feature extraction from qdec output
by Damien MARIE 29 Sep '16

29 Sep '16

Hi, Many thanks for your prompt reply Pr. Greve. I did : mri_glmfit --y /home/damien/bin/freesurfer/subjects/qdec/RH_Dys-CT_CSA_AgeGenderWRCSA/y.mgh --fsgd /home/damien/bin/freesurfer/subjects/qdec/RH_Dys-CT_CSA_AgeGenderWRCSA/qdec.fsgd dods --glmdir /home/damien/bin/freesurfer/subjects/qdec/RH_Dys-CT_CSA_AgeGenderWRCSA --surf fsaverage rh --label /home/damien/bin/freesurfer/subjects/fsaverage/label/rh.aparc.label --C /home/damien/bin/freesurfer/subjects/qdec/RH_Dys-CT_CSA_AgeGenderWRCSA/contrasts/rh-Avg-Intercept-area.mat --C /home/damien/bin/freesurfer/subjects/qdec/RH_Dys-CT_CSA_AgeGenderWRCSA/contrasts/rh-Diff-dyslexic-control-Intercept-area.mat --C /home/damien/bin/freesurfer/subjects/qdec/RH_Dys-CT_CSA_AgeGenderWRCSA/contrasts/rh-Diff-male-female-Intercept-area.mat --C /home/damien/bin/freesurfer/subjects/qdec/RH_Dys-CT_CSA_AgeGenderWRCSA/contrasts/rh-X-group-gender-Intercept-area.mat --eres-save mri_segstats --in /home/damien/bin/freesurfer/subjects/qdec/RH_Dys-CT_CSA_AgeGenderWRCSA/eres.mgh --sum toto --annot fsaverage rh mc-z.abs.th23.sig.ocn --avgwf RH_Dys-CT_CSA_AgeGenderWRCSA.dat 1) I don’t get it though. Probably I made a bad description of my goal, perhaps using this terminology of “residuals” also is not very accurate. I exported the txt file (output of mri_segstats computed on eres.mgh) to a statistical software and ran a mancova per cluster on cluster values with covariatess : age, right hemispheric surface area + gender factor. I find significant effects of the covariates on 7/9 clusters. I was not expecting such effects. I wanted to extract residuals of surface area in the significant clusters obtain using the Qdec Monte Carlo simulation on the contrast of interest (Dys - Ct) after removing all covariate effects. My aim was to look at the differences between the two levels of the factor of interest to get a sense of what is happening in this Qdec analysis and this particular contrast of interest. These results are in an opposite direction in comparison with other Qdec analysis without covariates / ROI analysis on surface area residuals after removing effect of gender, age and right hemispheric surface area (Destrieux's labels) / Whole-brain VBM analyses with covariates (not on surface area then...) Basically I have the feeling there is something wrong with the contrast display in this particular qdec analysis. I don’t know how I could get what I called the CSA residuals in the framework of this analysis. 2) Another question: should I standardize or center my covariates before proceeding to the analysis? 3) A silly question probably but to be 100% sure… If in the qdec.table.dat, order of subjects is first group “ dys “ then second group “ ct “ and that the contrast is called: rh-Diff-dys-dyslexic-control-intercept-area , negative p value means decrease of surface area in the first group (dys) as compared to the second group (ct), right ? Thank you and best, Damien MARIE Douglas Greve <http://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=from:…> Wed, 28 Sep 2016 12:40:51 -0700 <http://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=date:…> Those are not residuals. If you want residuals, you will need to run mri_glmfit from the command line adding --eres-save. You can get the command line from the mri_glmfit.log file in the glmdir On 9/28/16 10:58 AM, Damien MARIE wrote: Dear FreeSurfers, Sorry for the repost. I’m still trying to extract the residuals of cortical surface area from a qdec analysis with two factors (2 levels) and 2 covariates. I tried this command line: mri_segstats --in /home/damien/bin/freesurfer/subjects/qdec/RH_Dys-CT_CSA_AgeGenderWRCSA/y.mgh --sum toto --annot fsaverage rh mc-z.abs.th23.sig.ocn --avgwf RH_Dys-CT_CSA_AgeGenderWRCSA.dat I’ve got a text file with 9 columns (number of clusters) and 69 lines (number of subjects). Now I am not 100% sure it’s really the residuals (y.mgh) so I would be glad if somebody could tell me please. Best, Damien Original post: Dear experts, I would like to know what is the best and simplest way to extract cortical surface area and thickness from clusters obtained after a Monte Carlo correction. This is a group comparison I did with qdec including gender as discrete variable + age and mean thickness or whole hemispheric surface area as nuisance factors, so I would like to get the feature residuals after the removal of the covariate effects. I am sorry, I saw several posts about that but for me it’s not completely clear what command line I should use to get tables for this… Thank you and best, Damien *Damien MARIE*

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VM box installation error
by Arshad Zaman 29 Sep '16

29 Sep '16

Hi, I am a new user and trying to install Freesurfer using the virtualbox installation instructions (windows 7). I have created the virtual machine and can view the VB manager with the correct specific (general, system, display, etc) using the freesurfer image (freesurfer*.vdi). The FreeSurfer5.3 machine is running however the pop-up box displays, error: file not found. grub rescue> Any suggestions will be most appreciated (to save me hours of painful trial and error attempts!), Best wishes, Arshad

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tksurfer viewing issues
by Paige Scalf 29 Sep '16

29 Sep '16

Hello, I too am having trouble with tksurfer displaying the surfaces upside down and back to front, but believing that they are correctly oriented (i.e. Talairach coordinates change in the wrong direction wrt to the surface but in the correct direction wrt the display window). I"m also running a CentOs flavor. Did anyone manage to solve this issue? All the best, Paige

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mgz file format
by prasser 29 Sep '16

29 Sep '16

Hi, When using mri_convert to create 001.mgz from dicom that have *not* been anonymized does any patient, institution, study description etc information get transferred into the 001.mgz? Thanks.

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trac-all -path Segmentation fault
by Lars M. Rimol 29 Sep '16

29 Sep '16

Hi, I ran trac-all -prep and bedpostx successfully and qc (in accordance with tutorial) was fine but trac-all -path failed, due to "Segmentation fault" on two subjects: Segmentation fault Linux compute-16-6.local 2.6.32-573.18.1.el6.x86_64 #1 SMP Tue Feb 9 22:46:17 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux trac-paths exited with ERRORS at ti. 20. sep. 09:40:55 +0200 2016 --------- Segmentation fault Linux compute-16-14.local 2.6.32-573.18.1.el6.x86_64 #1 SMP Tue Feb 9 22:46:17 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux trac-paths exited with ERRORS at ti. 20. sep. 09:30:07 +0200 2016 Where do I go next? sincerely yours, Lars M. Rimol, PhD Senior researcher, Norwegian Advisory Unit for functional MRI Department of Radiology, St. Olav's University hospital, 7006 Trondheim, Norway

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Sulcus depth
by Hanbyul Cho 28 Sep '16

28 Sep '16

Dear FreeSurfer Team, I have questions about the sulcal depth. 1) I heard that the output/surf/?h.sulc is showing the sulcal depth. Is it correct that the sulcal depth measure unit is normalized z-score, mm? And is it correct that the (-) values of sulcal depth mean gyral region (green), and (+) values mean sulcal region (red)? 2) I wonder if ?h.sulc is based on white matter surface or pial matter surface. 3) I analyzed the sulcal depth by vertex-level. if the results include the sulc (-) values region, Is it meaning that the gyral height? 4) I wonder the method/commands for extracting the sulc value by label-level. 5) Could you let me know the recommended smoothing option if it possible? (e.g. --fwhm-trg [N]) I appreciate your help. Thank you. Han Byul Cho

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Co-registering different source data
by Crawford, Anna 28 Sep '16

28 Sep '16

Hello, I am trying to create a new surface area on the inflated brain given by freesurfer using recon-all. I make to create my own ROI that is co-registered onto this surfer. Ultimately, I want to be able to take information from a different data source such as EEG and have it co-registered onto the inflated surface. How do I go about creating this new ROI surface? Thanks, Anna =================================== Please consider the environment before printing this e-mail Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & World Report (2015). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. Confidentiality Note: This message is intended for use only by 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 the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. Thank you.

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Freesurfer compliant pediatric brain template for pediatric brain segmentation using reconall
by GAJENDRA KATUWAL (RIT Student) 28 Sep '16

28 Sep '16

Hello FreeSurfers, I am considering using Freesurfer recon-all for segmentation of T1 brain MRIs of young subjects (1-4 years). I am planning to use a Freesurfer compliant pediatric template to maximize the segmentation accuracy. In the publication titled *A FreeSurfer-compliant consistent manual segmentation of infant brains spanning the 0–2 year age range (* https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4332305/) by *Katyucia de Macedo Rodrigues, Emma Ben-Avi, Danielle D. Sliva, Myong-sun Choe, Marie Drottar, Ruopeng Wang, Bruce Fischl, Patricia E. Grant,and Lilla Zöllei, * it has been mentioned that "Furthermore, we are also planning on making an atlas generated from our training data sets available to the scientific community (as part of the FreeSurfer package), which can serve as a template in structural and functional studies and as a teaching tool for trainees." Has the pediatric template been released yet? Is there anyway the pediatric template can be accessed if it has been released? Is it available in the dev version or upcoming Freesurfer 6? Regards, Gajendra Jung Katuwal PhD Candidate in Imaging Science

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optseq help
by Alexandre Obert 28 Sep '16

28 Sep '16

Dear all, I would like to optimize my design by inserting null-events between my trials (in order to better catch the HRF shape with reasonable duration of the experiment) using optseq. I'm not very familiar with this useful tool and I wonder if you could check my setup? Here my design : I've got 12 trials per run (2 runs per participants). Each of my trial is 34s long and is composed as follow : -An instruction reminder screen of 4s -A video stimulus of 12s to 20s. This screen will be my "stimulus of interest". It's followed by a fixation cross in such a way that their cumulated durations will not exceed 20s -A question about the video followed by a fixation cross in such a way that their cumulated durations will not exceed 20s. -A jitter (a fixation cross), determined by optseq It's a 2 (A1; A2) x2 (B1; B2) design and I'm interested in these following contrasts: A1 vs A2 B1 vs B2 (The interaction contrast will have an exploratory value in my analysis.) In order to determine the jitters and the order of the stimuli, I set the optseq as follow: --ntp 210\ --tr 2\ --psdwin 0 40 1\ --ev evA1B1 34 3\ --ev evA1B2 34 3\ --ev evA2B1 34 3\ --ev evA2B2 34 3\ --ecv 1 1 -1 -1\ --evc 1 -1 1 -1\ --nsearch 10000\ --nkeep 3 I'm not very confident with my setup and if it's correct? I also wonder if I correctly set the ev durations and the psdwin. The stimulus of interest is the video but I set the ev using the trial duration in order to obtain ITI jitters and psdwin to the trial duration. This results in a poor efficiency and I wonder if it's possible to better optimized this design... Any help will be appreciated... Regards, Alexandre

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