Freesurfer November 2014

freesurfer@nmr.mgh.harvard.edu

99 participants
144 discussions

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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Re: [Freesurfer] ADNI protocol anisotropic resolution
by Antonio Algaze Beato 19 Nov '14

19 Nov '14

Thank you very much for your response. Out of curiosity, does someone know why the ADNI protocol has an anisotropic voxel resolution? I was wondering if it had to do with the increased SNR being more beneficial for accurate segmentation than the gain in resolution from a 1mm isotropic voxel... or, perhaps it is meant to speed things up and and cover the whole brain a bit quicker? Cheers, Antonio On Wednesday, November 19, 2014, Antonio Algaze Beato < antonio.algaze(a)upr.edu> wrote: > Dear group, > > I am new to FS and the ADNI protocol, thus my question: is it ok to have a > slice thickness of 1.2 mm and in-plane resolution of 1.05 mm for cortical > segmentation and brain volume analyses? This seems to be a sequence > suggested on the FreeSurferWiki (I am using a GE750 3T). > > Doesn't the anisotropic resolution introduce a bias? > > Thanks a lot! > > > > > -- > Antonio Algaze, PhD > University of Puerto Rico > Physics, UPR-Bayamón > Radiology, UPR-School of Medicine > >

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multiple comparisons compensation for first-level analysis
by Milde, Christopher 19 Nov '14

19 Nov '14

Dear Freesurfer experts, I'm not sure how to apply cluster-wise correction for multiple comparisons when one is not interested in doing group statistics. For group analysis you concatenate individuals into one file and use mri_glmfit and mri_glmfit-sim to run general linear model and simulations. I want to apply multiple comparisons only within the individual subjects (stay at first-level), so that I don't have glm directories created by mri_glmfit. I ran recon-all with -qcache, so I have pre-computed MC simulations. I used the -fwhm option during selxavg3-sess to estimate smoothness. è pre-cached simulation I have fMRI-data. Do you have any suggestions? Sincerely yours, Christopher

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ADNI protocol anisotropic resolution
by Antonio Algaze Beato 19 Nov '14

19 Nov '14

Dear group, I am new to FS and the ADNI protocol, thus my question: is it ok to have a slice thickness of 1.2 mm and in-plane resolution of 1.05 mm for cortical segmentation and brain volume analyses? This seems to be a sequence suggested on the FreeSurferWiki (I am using a GE750 3T). Doesn't the anisotropic resolution introduce a bias? Thanks a lot! -- Antonio Algaze, PhD University of Puerto Rico Physics, UPR-Bayamón Radiology, UPR-School of Medicine

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intersection pial & pial-outer-smoothed
by Octavian Lie 19 Nov '14

19 Nov '14

Dear All, The ?h.pial and its corresponding ?h.pial-outer-smoothed surface in a subject with a well reconstructed pia are intersecting, see attached (green- pial, gray- smoothed pia). 1. Is this expected? and 2. Can the ?h.pial-outer-smoothed constrained by a command flag to strictly encompass pia and not intersect it? Thank you, Octavian

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How does freesurfer smoothes the data?
by ye tian 18 Nov '14

18 Nov '14

Hello freesurfers, I would like to understand intuitively how data is smoothed by Freesurfer. Is it an analogue to kernel smoothing, with the different FWHM equivalent to different bandwidths? Thank you very much! Sincerely, Ye

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Freesurfer November 2014