Freesurfer

freesurfer@nmr.mgh.harvard.edu

19 participants
30132 discussions

mri_convert GradFile
by Steven Swinford 28 Sep '10

28 Sep '10

Hi FreeSurfer gurus, I'm trying to run a diffusion analysis on some old scans and am running into this error during mri_convert: ERROR: cannot open /usr/local/freesurfer/stable5/diffusion/mgh-dti-seqpack/gradient_mgh_dti06.gdt I noticed that stable4 has the GradFile with this naming convention, but stable5 only has a GradFile that omits the leading 0. usr/local/freesurfer/stable5/diffusion/mgh-dti-seqpack/gradient_mgh_dti6.gdt Are these the same GradFiles? Is there a way run these old scans through stable5 without this error? Thanks for your help, Steven

2 5

Re: [Freesurfer] Space of FreeSurfer Stats
by Douglas N Greve 28 Sep '10

28 Sep '10

Hi Tyler, I'm not sure what you mean by the stats being in a particular space. I had understood it to mean the space that volumes would be measured in. Is that right? If so, then the volumes will be measured in the space of the input, whatever input you supplied. doug ps. I'm copying the freesurfer list here so that others may benefit from the answer and so that the answer (not just the question) are searchable in are archive. blazey(a)artsci.wustl.edu wrote: > Hi Doug, > > Thank you for your quick response. I realize now, however, that my > question didn't quite get at what I was asking. What I meant to ask was > whether or not the stats outputted by FreeSurfer are in input space, not > whether they were in native space per se. So if I were register a session > to an atlas before putting it through FreeSurfer, would FreeSurfer output > stats in my atlas space? Sorry for my mistake and thanks again. > > - Tyler > > >> yes, they are measured in native space. >> >> doug >> >> blazey(a)artsci.wustl.edu wrote: >> >>> Hi All, >>> >>> Are the volume stats outputted by FreeSurfer in native space or in >>> FreeSurfer's space? According to some older mailing list questions, they >>> are in native space, but I wanted to make sure that this was still the >>> case. Thanks in advance for any help. >>> >>> - Tyler >>> >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer(a)nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >>> >>> >>> >> -- >> Douglas N. Greve, Ph.D. >> MGH-NMR Center >> greve(a)nmr.mgh.harvard.edu >> Phone Number: 617-724-2358 >> Fax: 617-726-7422 >> >> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >> FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html >> >> >> >> 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. >> >> > > > > -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html

2 1

Space of FreeSurfer Stats
by blazey＠artsci.wustl.edu 28 Sep '10

28 Sep '10

Hi All, Are the volume stats outputted by FreeSurfer in native space or in FreeSurfer's space? According to some older mailing list questions, they are in native space, but I wanted to make sure that this was still the case. Thanks in advance for any help. - Tyler

2 1

error in recon-all -autorecon3
by Paola Valsasina 28 Sep '10

28 Sep '10

Dear FS list, I am trying to finish my first analyses with freesurfer; however, I have some problems when running the last stages of recon-all. In summary what I did: 1) recon-all -autorecon1 (worked well) 2) some minor brain strip editing 3) recon-all -autorecon2 (worked well) 4) some editing both of white matter and adding some control points 5) Now I have run recon-all -autorecon2-cp -autorecon3, but I receive the following error (after many hours of post-processing): mris_volmask -label_left_white 2 -label_left_ribbon 3 -label_right_white 41 -label_right_ribbon 42 -save_ribbon -save_distance "subject_name" mris_volmask.bin: error while loading shared libraries: libtiff.so.3: cannot open shared object file: No such file or directory recon-all exited with errors Apparently, cortical segmentation has been performed, since I see in the stats folder both ?h.aparc.stats and ?h.aparc.a2009s.stats files. Which additional output am I missing because of this error? Thank you for your help Paola Paola Valsasina Research Fellow to Prof. M. Filippi Neuroimaging Research Unit Institute of Experimental Neurology Hospital San Raffaele via Olgettina 60 20132 Milan - ITALY

2 1

Re: [Freesurfer] Freesurfer Digest, Vol 79, Issue 32
by Siti Hajar 28 Sep '10

28 Sep '10

When I ran this command, " mri_segstats --seg "$fsaveragesurfpath"/"$hemi".fsaverage."$hemi"_"$roi"_"$subj".mgh --in "$hemi".thickness.fsaverage.mgh --sum segstats-"$hemi"_"$roi"_"$subj".txt, this kind of output came out "mghRead(/usr/local/freesurfer/subjects/100905lsy/surf/lh.thickness.fsaverage.mgh, -1): could not open file--> which indicated that there was no lh.thickness.fsaverage.mgh created. Well, basically, when I ran recon-all, lh.thickness.fsaverage.mgh should be created, but it wasn't. So, again with my question,is this situation happened due to the new freesurfer software that I installed or was it caused by other source? Thank you ________________________________ From: "freesurfer-request(a)nmr.mgh.harvard.edu" <freesurfer-request(a)nmr.mgh.harvard.edu> To: freesurfer(a)nmr.mgh.harvard.edu Sent: Mon, September 20, 2010 9:49:16 PM Subject: Freesurfer Digest, Vol 79, Issue 32 Send Freesurfer mailing list submissions to freesurfer(a)nmr.mgh.harvard.edu To subscribe or unsubscribe via the World Wide Web, visit https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer or, via email, send a message with subject or body 'help' to freesurfer-request(a)nmr.mgh.harvard.edu You can reach the person managing the list at freesurfer-owner(a)nmr.mgh.harvard.edu When replying, please edit your Subject line so it is more specific than "Re: Contents of Freesurfer digest..." Today's Topics: 1. Re: mri_label2volume issues (Michael Waskom) 2. Generating a 'non-zero' group mask (Marco Loggia, PhD) 3. Re: recon-all quality control checks on large numbers of subjects (Nick Schmansky) 4. lh.thickness.fsaverage (Siti Hajar) 5. Re: lh.thickness.fsaverage (Douglas Greve) ---------------------------------------------------------------------- Message: 1 Date: Fri, 17 Sep 2010 11:04:00 -0400 From: Michael Waskom <mwaskom(a)mit.edu> Subject: Re: [Freesurfer] mri_label2volume issues To: Freesurfer(a)nmr.mgh.harvard.edu Message-ID: <AANLkTi=5ZnihXybQu0Wwf-ysJN6oPoQk2bFuf2_iirzb(a)mail.gmail.com> Content-Type: text/plain; charset=ISO-8859-1 Hi Prapti, Basically, you just need to have a label file that you can turn into a lh.your_annot_name.annot (assuming your actual ROI is in the right hemisphere), so that mri_label2annot runs properly. The easiest thing to do would be to rename any old label you have in your subject's label directory to lh.dummy.label, and then create an annotation from that label with mri_label2annot. Then run mris_aparc2aseg as you tried to do before, which will create a volume that has 0's everywhere except in the area where your actual and dummy labels were projected. Figure out the voxel values for the ROI you want (using Freeview or tkmedit), and then run: mri_binarize --i your_annot_name+aseg.mgz --match <that voxel value> --o you_roi_name.mgz Which will have 1s where your ROI is and 0s everywhere else. Best, Mike -------Original Message------- Hi Doug, Thanks for the reply. I am sorry, I am a bit confused about what you mean by creating a dummy label. I am also not sure at which step I need to do this. As I understand it, I use mri_label2annot to transform my label into a annotation file and this will be separate for the two hemispheres. Do I then edit these files ? where exactly do I use mri_binarize? Thanks, Prapti -----Original Message----- From: Douglas N Greve [mailto:gr...@nmr.mgh.harvard.edu] Sent: Friday, 17 September 2010 12:44 AM To: Prapti Gautam Cc: freesurfer(a)nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mri_label2volume issues Right, I see, mri_aparc2aseg is hard-coded to expect both lh and rh. The easiest thing is to make a dummy label for the other hemisphere. In the final segmentation, left hemisphere will have an index of 1000+something, the right will have 2000+something. You can then use mri_binarize with --match create a new binary volume with just your hemisphere. doug Prapti Gautam wrote: > Hi Doug, > > Thanks for the reply. I have tried using the method you've suggested, > however, I'm stuck because mri_label2annot which I use to turn my label > into a annot file only works in one hemisphere while mri_aparc2aseg > works for the whole brain. Do you know a work around for this? > > Can I merge the annot files created from each hemisphere so that I can > pass it to mri_aparc2aseg? > > > Thanks, > > Prapti > > > ------------------------------ Message: 2 Date: Fri, 17 Sep 2010 11:38:22 -0400 From: "Marco Loggia, PhD" <marco(a)nmr.mgh.harvard.edu> Subject: [Freesurfer] Generating a 'non-zero' group mask To: <freesurfer(a)nmr.mgh.harvard.edu> Message-ID: <5EA6CF4FA3914BC49D4CC51BD03A8618@MARCOWORK> Content-Type: text/plain; charset="us-ascii" Dear all, I am performing surface analyses on ASL CBF maps. As these maps do not cover the whole brain, and some masks have larger brain coverage than others, I would need to create a binary surface mask (in the fsaverage space) which would zero out the vertices where at least one of my subjects have a zero value. This map would then be used to spatially limit my statistical analyses in mri_glmfit. Any suggestions? Thanks a lot, Marco _____________________ Marco L. Loggia, PhD Postdoctoral Fellow, Mass General Hospital & Brigham and Women's Hospital Harvard Medical School CNY Building 120, suite 101E Charlestown, Massachusetts 02129 Phone: (617) 643-7267 Fax: (617) 643-7340 marco(a)nmr.mgh.harvard.edu

1 0

Pial Edit on Atrophied Brain
by Soon Hock Wei 27 Sep '10

27 Sep '10

2 2

Mapping asymmetry on single hemisphere inflated surface
by Lena Palaniyappan 27 Sep '10

27 Sep '10

I want to compare vertexwise differences in thickness between R and L hemisphere in two groups is there any workaround to create a statistical asymmetry map for this purpose? Cheers Lena _______________________________________________________ Lena Palaniyappan Clinical Lecturer & Honorary StR | Division of Psychiatry ( University of Nottingham) South Block 'A' floor| Queens Medical Centre | Nottingham | NG7 2UH This message and any attachment are intended solely for the addressee and may contain confidential information. If you have received this message in error, please send it back to me, and immediately delete it. Please do not use, copy or disclose the information contained in this message or in any attachment. Any views or opinions expressed by the author of this email do not necessarily reflect the views of the University of Nottingham. This message has been checked for viruses but the contents of an attachment may still contain software viruses which could damage your computer system: you are advised to perform your own checks. Email communications with the University of Nottingham may be monitored as permitted by UK legislation.

2 1

QDEC table loading errors
by James Porter 27 Sep '10

27 Sep '10

3 4

pericalcarine cortex - subdivision
by Pedro Paulo de Magalhães Oliveira Junior 27 Sep '10

27 Sep '10

I have a fMRI study where I need to quantify activation in the pericalcarine_LH and pericalcarine_RH. The problem I'd like to solve is to subdivide pericalcarine_LH and pericalcarine_RH in its superior and inferior parts. Is there any automatic way to make this subdivision? thanks Pedro Paulo Jr --------------------------------------------------------------------- Pedro Paulo de Magalhães Oliveira Junior Diretor de Operações Netfilter & SpeedComm Telecom -- www.netfilter.com.br -- For mobile: http://www.netfilter.com.br/mobile

3 6

Re: [Freesurfer] preproc-sess failing
by Adam Nitenson 27 Sep '10

27 Sep '10

Hi Doug, My original email was sent to the freesurfer list. Here is the more detailed terminal info: FREESURFER_HOME: /usr/local/freesurfer/stable4 Build stamp: freesurfer-Linux-centos4_x86_64-stable-v4.5.0-20100311 RedHat release: CentOS release 5.5 (Final) Kernel info: Linux 2.6.18-194.8.1.el5 x86_64 NMR Center info (/space/freesurfer exists): machine: audrey SUBJECTS_DIR: /cluster/roffman/users/MTH_Study PWD: /cluster/roffman/users/MTH_Study ssh audrey setenv SUBJECTS_DIR /cluster/roffman/users/MTH_Study cd /cluster/roffman/users/MTH_Study I had already ran all of the unpacking commands through recon-all without fail (see old email below for first subject; MTH20007AA). These were done using the SUBJECTS_DIR /autofs/space/seymour_001/users/MTH_Study. After that, we had bought a TB in the new cluster, and I copied all of the seymour 1 data there. So, I then switched to SUBJECTS_DIR: /cluster/roffman/users/MTH_Study, as running the preproc-sess for the other subject using the directory /cluster/roffman/users/folate_subjects worked fine. The failed command was: preproc-sess -s MTH20007AA -fwhm 5 with the error: niiRead(): error reading from 012/fmc.nii ERROR: Read 40, expected 64 ERROR: mri_fwhm failed ERROR: spatialsmooth-sess failed -Adam > Hi Adam, what is the command line you ran and the directory you ran it > from? What was your SUBJECTS_DIR? In general, you should send this > information each time you write. You might want to look at > surfer.nmr.mgh.harvard.edu/fswiki/BugReporting for other ways to improve > your bug reports. Also, please start to send these kinds of things to > martinos-tech or the freesurfer list. > > thanks > > doug > > > Adam Nitenson wrote: >> Hi Doug, >> >> Using the new storage cluster with extra space allows the second >> subject, FB0011060AA to preprocess, but I'm still having issues with >> the first MTH20007AA. I'm getting the following error now: >> >> niiRead(): error reading from 012/fmc.nii >> ERROR: Read 40, expected 64 >> ERROR: mri_fwhm failed >> ERROR: spatialsmooth-sess failed >> >> Again, the raw data source is >> /cluster/archive/288/siemens/TrioTim-35101-20100916-143244-437000 >> >> -Adam >> >> >> >> >>> Ah, yea, it's probably space issues. Let me know if more space does >>> not fix the problem. >>> >>> doug >>> >>> On 9/23/10 7:37 AM, Adam Nitenson wrote: >>> >>>> Sure. I would also like to note that after I sent that email, I >>>> realized >>>> that I only had 508 KB left in Seymour 1, so I don't know if these >>>> errors >>>> could have been generated due to a lack of space. We just purchased a >>>> block of space on the new storage cluster, but haven't used it yet. >>>> >>>> If you think it might still be something else....here are the commands >>>> (after sourcing, etc). >>>> >>>> FIRST SUBJECT >>>> >>>> unpacksdcmdir -src >>>> /cluster/archive/288/siemens/TrioTim-35101-20100916-143244-437000 >>>> -targ >>>> /autofs/space/seymour_001/users/MTH_Study/MTH20007AA -run 5 MPRAGE COR >>>> blah >>>> >>>> unpacksdcmdir -src >>>> /cluster/archive/288/siemens/TrioTim-35101-20100916-143244-437000 >>>> -targ >>>> /autofs/space/seymour_001/users/MTH_Study/MTH20007AA -fsfast -run 12 >>>> bold >>>> nii f.nii -fsfast -run 13 bold nii f.nii -fsfast -run 14 bold nii >>>> f.nii >>>> -fsfast -run 15 bold nii f.nii -fsfast -run 16 bold nii f.nii -fsfast >>>> -run >>>> 17 bold nii f.nii >>>> >>>> cd $SUBJECTS_DIR >>>> >>>> recon-all -i >>>> /autofs/space/seymour_001/users/MTH_Study/MTH20007AA/MPRAGE/005 -s >>>> MTH20007AA -force >>>> >>>> recon-all -autorecon-all -s MTH20007AA >>>> >>>> preproc-sess -s MTH20007AA -fwhm 5 (FAILED) >>>> >>>> >>>> SECONDS SUBJECT >>>> >>>> unpacksdcmdir -src >>>> /cluster/archive/288/siemens/TrioTim-35101-20100917-142812-643000 >>>> -targ >>>> /autofs/space/seymour_001/users/folate_subjects/FB0011060AA -run 5 >>>> MPRAGE >>>> COR blah >>>> >>>> unpacksdcmdir -src >>>> /cluster/archive/288/siemens/TrioTim-35101-20100917-142812-643000 >>>> -targ >>>> /autofs/space/seymour_001/users/folate_subjects/FB0011060AA -fsfast >>>> -run >>>> 13 bold nii f.nii -fsfast -run 14 bold nii f.nii -fsfast -run 15 bold >>>> nii >>>> f.nii -fsfast -run 16 bold nii f.nii -fsfast -run 17 bold nii f.nii >>>> -run >>>> 18 bold nii f.nii >>>> >>>> cd $SUBJECTS_DIR >>>> >>>> recon-all -i >>>> /autofs/space/seymour_001/users/folate_subjects/FB0011060AA/MPRAGE/005 >>>> -s >>>> FB0011060AA -force >>>> >>>> recon-all -autorecon-all -s FB0011060AA >>>> >>>> preproc-sess -s FB0011060AA -fwhm 5 (FAILED) >>>> >>>> Let me know if you need any more info. >>>> >>>> Thanks, >>>> >>>> Adam >>>> >>>> >>>>> Adam, can you send a pointer to the data to me? >>>>> >>>>> doug >>>>> >>>>> Adam Nitenson wrote: >>>>> >>>>>> Hello freesurfers, >>>>>> >>>>>> I am trying to unpack a couple of recent subjects in Stable 4. I ran >>>>>> all >>>>>> steps through recon-all without error. However, when I try to run >>>>>> the >>>>>> next >>>>>> step, preproc-sess, it keeps failing. >>>>>> >>>>>> This is the command I enter: >>>>>> >>>>>> preproc-sess -s FB0011060AA -fwhm 5 >>>>>> >>>>>> It works for about 30 seconds, and then I get the following in >>>>>> return >>>>>> >>>>>> niiRead(): bad number of dimensions (0) in >>>>>> 013/tmp.mc-afni2.15211/outvol.nii.gz >>>>>> reading info from 013/f.nii... >>>>>> $Id: mri_convert.c,v 1.146.2.5 2009/04/08 18:40:23 nicks Exp $ >>>>>> reading from 013/tmp.mc-afni2.15211/outvol.nii.gz... >>>>>> ERROR: converting output >>>>>> Invalid null command. >>>>>> ERROR: mc-sess failed >>>>>> >>>>>> the error for the other subject was slightly different: >>>>>> >>>>>> niiRead(): error reading from 013/tmp.mc-afni2.15452/outvol.nii.gz >>>>>> reading info from 012/f.nii... >>>>>> $Id: mri_convert.c,v 1.146.2.5 2009/04/08 18:40:23 nicks Exp $ >>>>>> reading from 013/tmp.mc-afni2.15452/outvol.nii.gz... >>>>>> ERROR: Read 14, expected 64 >>>>>> ERROR: converting output >>>>>> Invalid null command. >>>>>> ERROR: mc-sess failed >>>>>> >>>>>> Any idea what might be going on? I've done these same steps many >>>>>> times >>>>>> for >>>>>> processing data and have not before received this error. >>>>>> >>>>>> Thanks! >>>>>> >>>>>> Adam Nitenson, B.S. >>>>>> Brain Genomics Lab >>>>>> Massachusetts General Hospital >>>>>> _______________________________________________ >>>>>> Freesurfer mailing list >>>>>> Freesurfer(a)nmr.mgh.harvard.edu >>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>>> >>>>>> >>>>>> >>>>>> >>>>> -- >>>>> Douglas N. Greve, Ph.D. >>>>> MGH-NMR Center >>>>> greve(a)nmr.mgh.harvard.edu >>>>> Phone Number: 617-724-2358 >>>>> Fax: 617-726-7422 >>>>> >>>>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >>>>> FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html >>>>> >>>>> >>>>> >>>>> >>>> Adam Nitenson, B.S. >>>> Brain Genomics Lab >>>> Massachusetts General Hospital >>>> >>>> >>>> >>> >>> >> >> >> Adam Nitenson, B.S. >> Brain Genomics Lab >> Massachusetts General Hospital >> >> >> > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > greve(a)nmr.mgh.harvard.edu > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html > > > Adam Nitenson, B.S. Brain Genomics Lab Massachusetts General Hospital

2 2

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