Freesurfer

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30099 discussions

Repost: estimating lesion size on surface
by Timothy Meier 20 Nov '14

20 Nov '14

Hello, I just wanted to repost this to see if anyone had any thoughts on an appropriate 'lesion' size for a pothole analysis performed on the surface. We want to compare the average number of small surface lesions (estimated from cortical thickness) across single subjects for a control group relative to our patient group. We have done similar analyses in the volume for white matter, so one thought was to use that same lesion size. However, that requires estimating a surface area from our previously used volume. Any thoughts on how to approach this, or thoughts on an appropriate lesion size to use would be appreciated. Thanks, -Tim ---------------------------------------------------------------------- > > Message: 3 > Date: Thu, 30 Oct 2014 15:03:53 -0500 > From: Timothy Meier <tmeier(a)mrn.org> > Subject: [Freesurfer] Converting lesion volume to surface area > To: freesurfer(a)nmr.mgh.harvard.edu > Message-ID: > <CAGXOw+14YO4VBWUAA4YfzE7Gerxo-PG33FPCEmpm8PxpTpW= > CA(a)mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > Hello, > > Previously we have used a lesion of 128 microliters and have filtered out > anything smaller in volume than that for analyses (single subject "pothole" > analysis). Now we want to do something similar on the surface. So we need > to approximate the surface area of that 128 microliters when translated to > group analysis surface (fsaverage). > > 128 microliters is 128 data points in 1x1x1 resolution. Let's say those > data points only exist in the cortical ribbon volume. > > Question 1: How many of the 128 data points from cortical ribbon volume get > translated into surface space? What is the volume to surface translation > ratio? > > Question 2: Because we want to filter clusters with mri_surfcluster, we are > interested in the resulting area of our original 128 lesion. Therefore, how > much area is represented by each data point when translated onto the > surface? > > Is this simply "AvgVtxArea" of the inflated surface multiplied by the > number of data points that get translated from volume to surface? > > And what is the best way to answer these two questions from standard > Freesurfer output: > e.g. Should we calculate from the ("NumVert" "SurfArea" "GrayVol") columns > of the lh.aparc.stats file, get the mean of all SurfArea/GrayVol from > aparc.stats, and then multiple by our 128? > > Any thoughts or suggestions would be appreciated. > > Thanks, > Tim >

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Odd thing about mris_convert? Position changed from freesurfer format to .stl
by ting xu 20 Nov '14

20 Nov '14

Hi there, In my understanding, mris_convert does not change any information (vertices coordinates and triangles) during converting, right? However, I observed odd thing as bellow, Command I used:* mris_convert subjid/surf/lh.white subjid/surf/lh.white.stl* I convert the white surface to .stl format, then load original white surface and .stl file in freeview, with subjid/mri/brainmask.mgz as volume underlay. The shape of lh.white.stl mesh looks the same as original one, but the position of lh.white.stl has totally been displaced. I attached a screenshot (yellow one is original white surface, red one is .stl format one). I also used freesurfer_read_surf function to read the coordinates and the faces in matlab, then compare it to .stl coordinate, they are the same. I need to use .stl format for my analysis outside freesurfer, then convert result back to freesurfer format. I am worried whether this odd thing cause any problems? [image: Inline image 2] PS, if it is fsaverage template surface, no position shift after format transform. Many thanks if anyone help with this, Ting

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Re: [Freesurfer] FreeSurfer GUI tutorial
by Lilla Zollei 20 Nov '14

20 Nov '14

Hi Piotr, There are several tutorials that describe our standard data processing pipeline. You can start by looking at: http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial with "Introduction to Freesurfer" and "Analyzing the Individual Subject". If you have any further questions, please, send them to the freesurfer mailing list. Lilla On Thu, 20 Nov 2014, Piotr Konrad Chlebda wrote: > Hello, > I have downloaded and installed freesurfer(as VM for Windows), but I can not find any simple gui tutorial for it. I need to extract corpus callosum from DICOM pictures. I thought that freesurfer provide me with simple way to do that, but actually did not.Could you send me any easy step by step guide to perform > what I need, please ? > > Best regards, > > Piotr > > >

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mri_convert : no output & infinite loop
by Nooshin Zadeh 20 Nov '14

20 Nov '14

Dear FreeSurfer experts, I get a new message when I use "mri_convert" command to convert dicom to mgz. I used to apply this command before and there was no problem. I wonder what is the reason that I get the new message. In addition, it does not create mgz file, and goes to infinite loop. *mri_convert "/M1/t1_se_ax_5/IM-0004-0001.dcm" "/FS/M1/mri/orig/001.mgz"* mri_convert /M1/t1_se_ax_5/IM-0004-0001.dcm /FS/M1/mri/orig/001.mgz $Id: mri_convert.c,v 1.166.2.2 2010/08/10 19:11:50 greve Exp $ reading from /M1/t1_se_ax_5/IM-0004-0001.dcm... Getting Series No Scanning Directory INFO: Found 39 files in /Users/christine/Raw_Data/M226/t1_se_ax_5 INFO: Scanning for Series Number 5INFO: found 37 files in series INFO: loading series header info. I appreciate if you can advise me. Regards Nooshin PhD Candidate Departments of Electrical & Computer Engineering University of Miami Email: n.zadeh(a)miami.edu

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Multiple comparision method
by wangzhiwei3233 20 Nov '14

20 Nov '14

Hi freesurfer experts, Is there other methods for multiple comparison correction apart from Monte carlo simulation in Freesurfer? Thanks! zhiwei

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Re: [Freesurfer] Longitudinal analysis and hippocampal subfields
by Erik O'Hanlon 20 Nov '14

20 Nov '14

Hi Eugenio, Should I send the files via dropbox, as it appears that the last one I sent is waiting approval due to size etc. Thanks and sorry for the hassle Erik ________________________________________ From: Erik O'Hanlon Sent: 20 November 2014 15:51 To: Freesurfer support list Subject: RE: [Freesurfer] Longitudinal analysis and hippocampal subfields Hi Eugenio, Yes, it seems to have happened on a few cases, I've only started running it with the subfields and the jobs are running on a cluster so many have not run to end yet but al that have, exit with the error. I've attached the hippo_subfields-log you requested. As the other subfieldResults is quite large with subdirs, should I sent you a dropbox link? Thanks for help. Very much appreciated, Best regards Erik ________________________________________ From: freesurfer-bounces(a)nmr.mgh.harvard.edu [freesurfer-bounces(a)nmr.mgh.harvard.edu] on behalf of Eugenio Iglesias [e.iglesias(a)bcbl.eu] Sent: 20 November 2014 14:47 To: Freesurfer support list Subject: Re: [Freesurfer] Longitudinal analysis and hippocampal subfields Hi Erik, did you experience the same problem with any other cases? Also, do you think you could send us the log file [subjectdir]/scripts/hippo-subfields.log, as well as the contents of [subjectdir]/tmp/subrieldResults? Cheers, /Eugenio Juan Eugenio Iglesias Postdoctoral researcher BCBL www.jeiglesias.com www.bcbl.eu Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer ----- Original Message ----- From: "Erik O'Hanlon" <erikohanlon(a)rcsi.ie> To: "Freesurfer support list" <freesurfer(a)nmr.mgh.harvard.edu> Sent: Thursday, November 20, 2014 2:04:15 PM Subject: Re: [Freesurfer] Longitudinal analysis and hippocampal subfields Hi Martin, I appear to have run into an issue when processing longitudinal data with the -hippo-subfields command. I get the following error. I have run the process in the cross (independent) mode and it ran okay at each time point (I have two). Wrote out aseg_thresholded.mgz kvlMathematicalMorphology aseg_thresholded.mgz dilate 3 imageFileName: aseg_thresholded.mgz radius: 3 Using dilating filter itk::ExceptionObject (0x2ccf4d0) Location: "void itk::ImageFileWriter<TInputImage>::Write() [with TInputImage = main(int, char**)::ImageType]" File: /usr/pubsw/packages/itk/current/include/InsightToolkit/IO/itkImageFileWriter.txx Line: 271 Description: itk::ERROR: ImageFileWriter(0x2cb8880): Largest possible region does not fully contain requested paste IO regionPaste$ Dimension: 3 Index: 0 0 0 Size: 0 0 0 Largest possible region: ImageRegion (0x7fff9c9b02e0) Dimension: 3 Index: [0, 0, 0] Size: [0, 0, 0] failed to do kvlMathematicalMorphology aseg_thresholded.mgz dilate 3 Linux tcin-n08.cluster 2.6.18-274.18.1.el5 #1 SMP Thu Feb 9 12:20:03 EST 2012 x86_64 x86_64 x86_64 GNU/Linux recon-all -s sub040_tp1.long.sub040_T1_baseimage exited with ERRORS at Wed Nov 19 20:34:12 GMT 2014 For more details, see the log file /projects/pi-frodlt/HPC_11_00383/Freesurfer_ABD/sub040_tp1.long.sub040_T1_baseimage$ To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting Any ideas very much appreciated. Erik From: freesurfer-bounces(a)nmr.mgh.harvard.edu [freesurfer-bounces(a)nmr.mgh.harvard.edu] on behalf of Erik O'Hanlon [erikohanlon(a)rcsi.ie] Sent: 18 November 2014 20:42 To: Freesurfer support list Subject: Re: [Freesurfer] Longitudinal analysis and hippocampal subfields That's super! Thanks again Martin Best regards Erik From: freesurfer-bounces(a)nmr.mgh.harvard.edu [freesurfer-bounces(a)nmr.mgh.harvard.edu] on behalf of Martin Reuter [mreuter(a)nmr.mgh.harvard.edu] Sent: 18 November 2014 18:07 To: Freesurfer support list Subject: Re: [Freesurfer] Longitudinal analysis and hippocampal subfields Hi Erik, no need to re-run . no need even to do -all, just do the subfields. Best, Martin On 11/18/2014 12:57 PM, Erik O'Hanlon wrote: Thanks Martin, Could I also ask that if the -long command was run without the subfield option, is it best to delete the dir and rerun it or simply recur the command with the subfields option included (and that will continue on and run the remaining hippo camp things?). Thanks again for your help, very much appreciated. Best regards Erik From: freesurfer-bounces(a)nmr.mgh.harvard.edu [ freesurfer-bounces(a)nmr.mgh.harvard.edu ] on behalf of Martin Reuter [ mreuter(a)nmr.mgh.harvard.edu ] Sent: 18 November 2014 17:04 To: Freesurfer support list Subject: Re: [Freesurfer] Longitudinal analysis and hippocampal subfields Hi Erik, yes, you would do the subfields only in the -long. No need currently to include it in cross (independent) or base. Best, Martin On 11/18/2014 11:41 AM, Erik O'Hanlon wrote: Dear FS Experts, I'm running a longitudinal analysis and have run the individual time points using the hippocampal subfields. Do I also need to include the -hippo-subfields in the recon-all -long command too? Thanks in advance for any input. Kind regards Erik Erik O'Hanlon Postdoctoral researcher RCSI Psychiatry Royal College of Surgeons in Ireland Beaumont Road, Beaumont, D9, Ireland T: 8093740 E: erikohanlon(a)rcsi.ie W: www.rcsi.ie RCSI DEVELOPING HEALTHCARE LEADERS WHO MAKE A DIFFERENCE WORLDWIDE _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Dr. Martin Reuter Instructor in Neurology Harvard Medical School Assistant in Neuroscience Dept. of Radiology, Massachusetts General Hospital Dept. of Neurology, Massachusetts General Hospital Research Affiliate Computer Science and Artificial Intelligence Lab, Dept. of Electrical Engineering and Computer Science, Massachusetts Institute of Technology A.A.Martinos Center for Biomedical Imaging 149 Thirteenth Street, Suite 2301 Charlestown, MA 02129 Phone: +1-617-724-5652 Email: mreuter(a)nmr.mgh.harvard.edu reuter(a)mit.edu Web : http://reuter.mit.edu _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Dr. Martin Reuter Instructor in Neurology Harvard Medical School Assistant in Neuroscience Dept. of Radiology, Massachusetts General Hospital Dept. of Neurology, Massachusetts General Hospital Research Affiliate Computer Science and Artificial Intelligence Lab, Dept. of Electrical Engineering and Computer Science, Massachusetts Institute of Technology A.A.Martinos Center for Biomedical Imaging 149 Thirteenth Street, Suite 2301 Charlestown, MA 02129 Phone: +1-617-724-5652 Email: mreuter(a)nmr.mgh.harvard.edu reuter(a)mit.edu Web : http://reuter.mit.edu _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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. _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Longitudinal analysis and hippocampal subfields
by Erik O'Hanlon 20 Nov '14

20 Nov '14

Dear FS Experts, I'm running a longitudinal analysis and have run the individual time points using the hippocampal subfields. Do I also need to include the -hippo-subfields in the recon-all -long command too? Thanks in advance for any input. Kind regards Erik Erik O'Hanlon Postdoctoral researcher [cid:rcsi-logob489c8] RCSI Psychiatry Royal College of Surgeons in Ireland Beaumont Road, Beaumont, D9, Ireland T: 8093740 E: erikohanlon(a)rcsi.ie<mailto:erikohanlon@rcsi.ie> W: www.rcsi.ie<http://www.rcsi.ie> RCSI DEVELOPING HEALTHCARE LEADERS WHO MAKE A DIFFERENCE WORLDWIDE

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Frontal WM ROI
by Michele Cavallari 19 Nov '14

19 Nov '14

Hi, I am planning to perform some regional analysis of the frontal white matter as a whole, and asking here for suggestions/help. >From the FS output wmparc.mgz I could select and merge the following labels to define my ROI parsorbitalis [4019, 3019] parstriangularis [4020, 3020] lateralorbitofrontal [4012, 3012] medialorbitofrontal [4014, 3014] rostralmiddlefrontal [4027, 3027] frontalpole [4032, 3032] superiofrontal [4028, 3028] caudalmiddlefrontal [4003, 3003] paracentral [4017, 3017] parsopercularis [4018, 3018] postcentral [4022, 3022] precentral [4024, 3024] rostralantcingulate [4026, 3026] However, a non-negligible portion of the subcortical frontal WM is classified as unsegmented WM [5001, 5002] by FS. Would you recommend any other FS output or template/atlas that I could use for the purpose of measuring MRI signal in the frontal WM? Thanks

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mri_convert and MINC data
by Eve M. LoCastro 19 Nov '14

19 Nov '14

Dear FreeSurfer experts, There are some image processing tools from the MINC toolkit I have been testing out on some FreeSurfer files, that all require the image to be in MINC format. I am able to convert the *.mgz files to *.mgz, but I have been unable to perform the conversion in the other direction (MNC -> MGZ), as forewarned in the mri_convert help file. The error I get when attempting the conversion is "Not a netCDF file." (in full below) Would anyone have suggestions for a workaround to get the modified MNC file back into MGZ FreeSurfer format and in the correct orientation? Thank you for your time, Eve evl2001@jake:~/Desktop$ mri_convert -it minc head.mnc -ot mgz head.mgz mri_convert -it minc head.mnc -ot mgz head.mgz $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from head.mnc... ncopen: filename "/dir/head.mnc": Not a netCDF file miopen: MINC package entry point Error opening /dir/head.mnc mincRead(): error reading volume from file /dir/head.mnc Eve LoCastro Staff Associate IDEAL, Radiology Department Weill Cornell Medical College 515 E. 71st St S118 Tel: 212-746-1289 Fax: 212-746-4189 http://ideal-cornell.com/<http://ideal-cornell.com>

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Regarding mri_convert command
by Gunjan Gautam 19 Nov '14

19 Nov '14

Hello Sir, I'm using FreeSurfer through Virtual Box. I tried the below command for reslicing my volume according to a reference volume but the process gets stuck at " reading volume". *mri_convert A.nii.gz A.resliced.nii.gz -rl B.nii.gz* A: Volume to be resampled / resliced B: Reference Volume Error message is being shown like below: mri_convert a.nii a.resliced.nii -rl b.nii $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from a.nii... -------------------------------------------------------------------------- ERROR: Invalid FreeSurfer license key found in license file /home/bibl04/Data_Home/Desktop/freesurfer/license.txt 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. Actually, I have two volumes, belong to the same subject. One volume is the ground truth which will be considered as standard for the second volume which is the processed one or the extracted brain. To perform a perfect comparison between both volumes, these must generate equal number of slices in order to compare the corresponding slide. But here there is problem with my volumes, that is while performing slicing Ground Truth volume is generating 360 slice and processed volume is generating 181 slides. So comparison can't take place in this way. What all I need is to do the resampling or generating the 181 slides from the Ground Truth as well. Best Regards, Gunjan

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