Freesurfer

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30078 discussions

Projecting processed 4D functional data to individual surfaces
by Jared Zimmerman 29 Sep '16

29 Sep '16

Hi All, I'm trying to project some processed resting-state data onto the surface to run some surface based parcellations, and I'm running into a bit of difficulty. Basically I'm using bbregister to register my functional to the T1, then mri_vol2surf to project to the surface with the following pseudocode: bbregister --s subjID --mov /mov_dir/subjID_example_func_brain.nii.gz \ --reg /mov_dir/coreg/fs_ep2struct_fsl.dat \ --init-fsl --bold mri_vol2surf --src /mov_dir/filtered_func_residuals.nii.gz \ --out /mov_dir/filtered_func_residuals_fs6_lh_6mm_noreshape.mgh \ --srcreg /coreg/fs_ep2struct_fsl.dat --hemi lh \ --surf white --projfrac 0.5 --icoorder 6 --fwhm 6 --out_type mgh --noreshape The registration looks pretty good after I run bbregister, but what I get out from the mri_vol2surf seems weird. First of all, the dimensions are 112745 x 1 x 1 x 120, which seems odd. I'm forcing no reshaping, and from the help page it seems like the x-dim should be 40962 for icoorder=6. I have 120 frames in my input data, so that seems to be right, but I'm not sure where this dimension is coming from. I've also tried it with icoorder=4 and I get the same x-dim=112745 when I'm expecting 2562. I've also run these commands with various iterations e.g. reshaping, no smoothing, no projfrac, and I get the same thing every time. I'm also wondering how I should view these files to confirm that the surface projection has worked as I expect it if/when I am able to get the dimensions to be correct. I cannot open any of the projected functional files in either freeview or tksurfer, so it will be helpful to know how I might be able to view these time-series on the surface after I've succeeded in projecting them to that space. Any advice would be much appreciated Thanks, Jared

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Re: [Freesurfer] Infalted/Label
by Bruce Fischl 29 Sep '16

29 Sep '16

I'll cc the list, which I should have done the first time. No, you didn't do anything wrong. This is what mri_label2label should do - sample these locations onto the surface you specify and fill in the vertex indices. Check the output of label2label and see if it has values >= 0 cheers Bruce On Thu, 29 Sep 2016, Crawford, Anna wrote: > Hi, > > I just checked all the labels I created and they all have -1 in the first column (the file name ending in 'N' should be the one created from mri_label2label). So, I did something wrong when originally creating the label I assume. When I created it, under the ROI tab, I created a new one and then drew it in the viewer with a volume (I did both white matter and brain mask) also loaded. Was this wrong? > > Thank you, > Anna > ________________________________________ > From: Bruce Fischl [fischl(a)nmr.mgh.harvard.edu] > Sent: Thursday, September 29, 2016 12:00 PM > To: Crawford, Anna > Cc: Anna Crawford; Douglas N. Greve > Subject: RE: Infalted/Label > > Hi Anna > > the label you send me hasn't been sampled onto the surface, which is why > it kills the 5.3 freeview (this has been fixed in the upcoming 6.0). You > can tell this is the case as the first column has all -1. If it had been > sampled onto the surface these values would be in [0, nvertices]. > > Does you newer one have non-zero values in this column? > > cheers > Bruce > > On Thu, 29 Sep 2016, > Crawford, Anna wrote: > >> It is in the left hemisphere. >> ________________________________________ >> From: Bruce Fischl [fischl(a)nmr.mgh.harvard.edu] >> Sent: Thursday, September 29, 2016 10:38 AM >> To: Anna Crawford >> Cc: Crawford, Anna; Douglas N. Greve >> Subject: Re: Infalted/Label >> >> are the labels lh or rh? >> On Wed, 28 Sep 2016, Anna Crawford wrote: >> >>> Hopefully this works better for you. Thank you, >>> >>> Anna >>> >>> >> >> >> 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. >> >> >> =================================== >> >> >> 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. >> >> >> > > =================================== > > > 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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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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