Freesurfer

freesurfer@nmr.mgh.harvard.edu

16 participants
30084 discussions

Re: [Freesurfer] Sulcal depth units (Simon Vandekar)
by Simon Vandekar 22 Jan '16

22 Jan '16

Hi Bruce, The units are not standardized because the standard deviation across the surface does not equal 1. >From line 227 in mris_inflate.c it says that the sulc file is demeaned before it is written out: MRISzeroMeanCurvature(mris) ; /* make sulc zero mean */ However I am still unclear on what the units are. They are too small to be millimeters. Given other published measurements of sulcal depth I think they might be in centimeters, but can you confirm? Thanks again, Simon >Hi Simon > >I just took a look at the code and I believe that we make it 0 median >(not mean) and unit standard deviation. The curvatures can get quite large >in regions where the vertex spacing is small and the median is robust to >this. > >cheers >Bruce > > >On Sat, 24 Oct 2015, Simon Vandekar wrote: > >> Hi Bruce, >> >> I think that unnormalized sulcal depth would be useful. However, I am also curious what the units are in the standard output, because they appear to not be z-score standardized in each hemisphere. >> >> Thanks again, >> Simon >> >> >>> H I Simon >>> Do you need the unnormalized sulc? It would be pretty easy to put something in to generate it >>> Bruce >>> >>>> On Oct 22, 2015, at 3:23 PM, Simon Vandekar <simonv(a)mail.med.upenn.edu> wrote: >>>> >>>> Hi Bruce, >>>> >>>> I chose a random subject from the ADNI dataset and computed the mean and variance for the left and right hemispheres separately. It looks like the mean is close to 0, however the variance is not 1. Do you think it is possible that the surfaces are demeaned, but the units are still something meaningful (i.e. not unitless)? >>>> >>>> >>>> sulc = read.table('rh.sulc.asc', header=FALSE, col.names=c('v', 'x', 'y', 'z', 'sulc')) >>>>> mean(sulc$sulc) >>>> [1] -1.236923e-08 >>>> >>>>> var(sulc$sulc) >>>> [1] 0.3276958 >>>> >>>>> quantile(sulc$sulc) >>>> 0% 25% 50% 75% 100% >>>> -1.72503 -0.42128 -0.03963 0.40072 1.80980 >>>> >>>> >>>> Thanks again, >>>> Simon >>>> >>>> >>>> >>>> >>>> >>>> Hi Simon >>>> >>>> they are originally mm, but I believe we z-score normalize them so that >>>> the sulc file is 0 mean and unit variance. >>>> >>>> cheers >>>> Bruce >>>> On Wed, 21 Oct 2015, Simon >>>> Vandekar wrote: >>>> >>>>> Dear Freesurfer experts, >>>>> >>>>> >>>>> I am reading the manuscript "Cortical Surface-Based Analysis II: Inflation, Flattening, and a Surface-Based Coordinate System" by Fischl, Sereno, and Dale (1999) where the estimation of sulcal depth is described on page 199, however from the description I am still unsure of the exact units of sulcal depth. >>>>> Are the units for sulcal depth in mm or are they in arbitrary units? >>>>> >>>>> Thanks in advance, >>>>> Simon

3 2

mkdir error when running FS 6.0 hippocampal segmentation
by Rosanna Olsen 21 Jan '16

21 Jan '16

Dear Dr. Eugenio Iglesias and FreeSurfer developers, Thank you for the development of this very useful segmentation tool! When I try to run FreeSurfer 6.0's hippocampal segmentation on our computing cluster, I get the following error: "error using mkdir; Permission denied". I am not sure which directory this part of the script is trying to write to (it might be the software directory where FreeSurfer is installed, in which I do not have write permission because it is on a shared resource) -- I will attach a screenshot of the error here. Your attention is appreciated! Thanks, Rosanna Olsen -- Rosanna Olsen, Ph.D. Scientist, Rotman Research Institute, Baycrest rolsen(a)research.baycrest.org http://research.baycrest.org/rolsen

1 0

12th International Summer School on Biomedical Imaging, Abbaye de Saint Jacut, Brittany, France, June 16-24, 2016. (fwd)
by Lilla Zollei 21 Jan '16

21 Jan '16

FYI: this is a great program for PhD students and postdocs. ---------- Forwarded message ---------- Date: Wed, 20 Jan 2016 17:09:55 +0100 From: Christian ROUX <christian.roux(a)mines-telecom.fr> To: ROUX Christian <c.roux(a)ieee.org> Subject: 12th International Summer School on Biomedical Imaging, Abbaye de Saint Jacut, Brittany, France, June 16-24, 2016. 12th International Summer School on Biomedical Imaging, Abbaye de Saint Jacut, Brittany, France, June 16-24, 2016. Dear former Faculty member of the summer school, This school has become the world reference in the field since its launching in 1994. As previous lecturer, you are acknowledged to have contributed to this success and the biomedical imaging community worldwide is grateful to your commitment. The organization of the 12th edition of the summer school to be held next June is progressing as you can see from our website (http://conferences.telecom-bretagne.eu/ieeess/ <http://conferences.telecom-bretagne.eu/ieeess/>) and the programme is already in a good shape. As you may remember, the summer school was originally located in Berder but has been relocated since 2014 in Saint Jacut de la Mer in a wonderful facility close to Saint Malo and Mont Saint Michel. The basic of the summer school remain the same: The students are about 45 (they are selected by an international committee) and usually come from more than 20 countries. They are PhDs, post-doctoral students, engineers from industry, and already involved in some area of biomedical imaging. The school is aimed at offering to the best international junior researchers a place for learning, exchanging and future networking. And we have the chance to gather the best experts in the world in this very active field who are keen to share their experience and interact with the students in many ways. We would be very honored and very pleased if you could help us in disseminating and publicizing the call for participation that is attached. As you know, we are currently in this critical phase of dissemination where it is of utmost importance to reach the students who might be interested in joining this fantastic adventure. Jean-Louis, Jean-Christophe and myself are looking forward to receiving your assistance in this matter. We take this opportunity to extend you our best wishes for a healthy and successful year 2016. Best regards. JLC & JCOM & ChR <http://www.mines-telecom.fr/> Prof. Christian ROUX Directeur de la recherche et de l’innovation / Executive Vice President for Research and Innovation +33 (0)1 45 81 71 7037-39 rue Dareau 75014 Paris, France <http://www.mines-telecom.fr/> <https://twitter.com/Mines_Telecom> <https://www.facebook.com/mines.telecom> <https://plus.google.com/+mines-telecomFr/> <https://www.linkedin.com/company/institut-mines-t-l-com> <http://blogrecherche.wp.mines-telecom.fr/>

1 0

tutorial assistance
by Jasmin Alves 21 Jan '16

21 Jan '16

Hello again freesurfer team, While running through the group analysis tutorial, on step "previously cached (qcached) Data I ran into the following issue with the command below. Any recommendations? Jasmins-MacBook-Pro:glm jasminalves$ mris_preproc --fsgd gender_age.fsgd --cache-in thickness.fwhm10.fsaverage --target fsaverage --hemi lh --out lh.gender_age.thickness.10.mgh & [2] 5633 Jasmins-MacBook-Pro:glm jasminalves$ ERROR: cannot find /buckner_data/tutorial_subjs/group_analysis_tutorial Thanks! Jasmin -- Jasmin Alves Predoctoral Student Medical Biology Graduate Program University of Southern California jalves(a)usc.edu

3 2

Regressing out various categorical variables
by Erik Lindberg 21 Jan '16

21 Jan '16

Dear Freesurfers, I am running a design in which I want to correct for a number of categorical variables: diagnosis, gender and apoe status and one continuous variable (age) in a correlation analysis Did I get this right? (below) Thanks, Eric GroupDescriptorFile 1 Title MyTitle Class AMCI_F_APOE- Class AMCI_F_APOE+ Class AMCI_MALE_APOE- Class AMCI_MALE_APOE+ Class CTL_FEMALE_APOE- Class CTL_FEMALE_APOE+ Class CTL_MALE_APOE- Class CTL_MALE_APOE+ Class NON_A_MCI_FEMALE_APOE- Class NON_A_MCI_FEMALE_APOE+ Class NON_A_MCI_MALE_APOE- Class NON_A_MCI_MALE_APOE+ Class SCI_FEMALE_APOE- Class SCI_FEMALE_APOE+ Class SCI_MALE_APOE- Class SCI_MALE_APOE+ Variables AGE_DEMEAN CSF_Ab40_ADx With the contrast matrix: corr.mtx: 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1

2 1

Freesurfer and Google Drive
by Arindam Chatterjee 21 Jan '16

21 Jan '16

Hello Freesurfer experts, Does anyone have experience running freesurfer on a mac, pointing to images stored on Google Drive? Due to space issues on disk, I was trying to take that approach, but when I run recon-all pointing to the image stack, I get errors - and it says "For more details, see the log file". Where is the log file stored that I can look at? Sorry - newbie questions... Ankita

3 4

Hippocampal subfields
by Alan Francis 21 Jan '16

21 Jan '16

Hi Eugenio: Hope all is well. I have a question. I have run the HSF algorithm on 32 brains and they ran smoothly without problems. I used only T1 scans. I did not have T2s. Now to extract the data, do I need to run the following: *<analysisID>.FSspace.mgz*: the additional scan, rigidly registered to the T1 data. *[lr]h.hippoSfLabels-<T1>-<analysisID>.v10.mgz*: they store the discrete segmentation volume at 0.333 mm resolution in the physical space of the FreeSurfer <https://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurfer> T1 data (and therefore of the aligned scan *<analysisID>.FSspace.mgz* as well). *[lr]h.hippoSfLabels-<T1>-<analysisID>.v10.1mm.mgz*: they store the discrete segmentation volume in the 1 mm FreeSurfer <https://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurfer> voxel space. *[lr]h.hippoSfVolumes-<T1>-<analysisID>.v10.txt*: these text files store the estimated volumes of the subfields and of the whole hippocampi. Or can I go directly to : quantifyHippocampalSubfields.sh <T1>-<analysisID> <output_file> <OPTIONAL_subject_directory> Thanks so much, best regards, Alan -- |~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~| *Alan N. Francis PhD* NIDA T32 Fellow in Computational Neuroscience Brain Imaging Center McLean Hospital Harvard Medical School 115 Mill Street, Belmont, MA 02478 alanf(a)bwh.harvard.edu <ezra_wegbreit(a)brown.edu> afrancis(a)mclean.harvard.edu |~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|

2 2

Analyze to nii convertor
by Mahmoudi, Fariborz 21 Jan '16

21 Jan '16

Dear All, I have a set of images with analyze 75 (img/hdr) format. I want to convert them to .nii single file format. I used the following command: mri_convert -i name_of_input_file -it analyze -ot nii -o name_of_output_file But the output file has not proper nii format, When I drag the file in the MRIcro I just see a single slice with scrambled picture. It is appreciated if anybody could help me and let me know which switches I should use. Thanks, Fari ________________________________ CONFIDENTIALITY NOTICE: This email contains information from the sender that may be CONFIDENTIAL, LEGALLY PRIVILEGED, PROPRIETARY or otherwise protected from disclosure. This email is intended for use only by the person or entity to whom it is addressed. If you are not the intended recipient, any use, disclosure, copying, distribution, printing, or any action taken in reliance on the contents of this email, is strictly prohibited. If you received this email in error, please contact the sending party by reply email, delete the email from your computer system and shred any paper copies. Note to Patients: There are a number of risks you should consider before using e-mail to communicate with us. See our Privacy & Security page on www.henryford.com for more detailed information as well as information concerning MyChart, our new patient portal. If you do not believe that our policy gives you the privacy and security protection you need, do not send e-mail or Internet communications to us.

4 4

Posterior Probability file for Hippocampal subfields segmentation
by Xinyang Feng 21 Jan '16

21 Jan '16

hi, FreeSurfer experts, I have a question about the new hippocampal subfields segmentation tool in FS 6.0. I wonder if there is an option to generate the posterior probability file like "posterior_right_CA1.mgz" generated in FS 5.3. Thanks, Xinyang

1 0

-hippocampal-subfields-T1 problem
by Carl Anderson 21 Jan '16

21 Jan '16

Hi All, I can't seem to get V6 hipposubfields to run on my new Yosemite install. Data was processed with V5.3 under 10.6.8. Attached log..but no error occurred. Thanks for your help! Carl <<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>> Carl M. Anderson, Ph.D. (mail stop 204) Assistant Professor of Psychiatry, Harvard Medical School & The Neuroimaging Center, McLean Hospital 115 Mill St. Belmont, MA 02478 Ph: 617-855-2972; Fax: 617-855-2770 e-mail: remfract(a)gmail.com; carl_anderson(a)hms.harvard.edu <<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>> Command line: vermisii:Only_5_3 carlanderson$ recon-all -s RB_139 -hippocampal-subfields-T1 INFO: FreeSurfer build stamps do not match Subject Stamp: freesurfer-Darwin-lion-stable-pub-v5.3.0 Current Stamp: freesurfer-Darwin-OSX-stable-v6-beta-20151015 INFO: SUBJECTS_DIR is /Applications/freesurfer/subjects/Only_5_3 Actual FREESURFER_HOME /Applications/freesurfer -rw-rw-r-- 1 carlanderson wheel 632773 Jan 21 09:41 /Applications/freesurfer/subjects/Only_5_3/RB_139/scripts/recon-all.log Darwin vermisii.mclean.harvard.edu 14.0.0 Darwin Kernel Version 14.0.0: Fri Sep 19 00:26:44 PDT 2014; root:xnu-2782.1.97~2/RELEASE_X86_64 x86_64 #-------------------------------------------- #@# Hippocampal Subfields processing (T1 only) left Thu Jan 21 09:57:22 EST 2016 \n /Applications/freesurfer/bin/segmentSF_T1.sh /Applications/freesurfer/MCRv80 /Applications/freesurfer RB_139 /Applications/freesurfer/subjects/Only_5_3 left \n See log file: /Applications/freesurfer/subjects/Only_5_3/RB_139/scripts/hippocampal-subfields-T1.log ------------------------------------------ Setting up environment variables --- DYLD_LIBRARY_PATH is .:/Applications/freesurfer/MCRv80/runtime/maci64:/Applications/freesurfer/MCRv80/bin/maci64:/Applications/freesurfer/MCRv80/sys/os/maci64: Warning: application is running on a locale different from the original platform locale. Registering imageDump.mgz to hippocampal mask from ASEG dyld: Library not loaded: /opt/local/lib/libgcc/libgomp.1.dylib Referenced from: /Applications/freesurfer/bin//kvlAutoCrop Reason: image not found /bin/bash: line 1: 5956 Trace/BPT trap: 5 /Applications/freesurfer/bin//kvlAutoCrop /Applications/freesurfer/subjects/Only_5_3/RB_139/tmp/hippoSF_T1_v10_left//hippoAmygBinaryMask.mgz 6 > /dev/null /Applications/freesurfer/bin//kvlAutoCrop /Applications/freesurfer/subjects/Only_5_3/RB_139/tmp/hippoSF_T1_v10_left//hippoAmygBinaryMask.mgz 6 >/dev/null: Trace/breakpoint trap /Applications/freesurfer/subjects/Only_5_3/RB_139/tmp/hippoSF_T1_v10_left//hippoAmygBinaryMask_autoCropped.mgz.gz: No such file or directory ERROR: problem reading fname SWITCH expression must be a scalar or string constant. Error in myMRIread>load_mgh (line 588) Error in myMRIread>myMRIread_aux (line 85) Error in myMRIread (line 56) Error in segmentSubjectT1_autoEstimateAlveusML (line 174) MATLAB:badSwitchExpression --

1 0

Jump to page:

2026

2025

2024

2023

2022

2021

2020

2019

2018

2017

2016

2015

2014

2013

2012

2011

2010

2009

2008

2007

2006

2005

2004

Freesurfer