Freesurfer

freesurfer@nmr.mgh.harvard.edu

30132 discussions

fix topology issue
by miracle ozzoude 01 Aug '17

01 Aug '17

Hello Freesurfer expert, While running recon-all on one of my subjects, the pipeline got stuck during the "fix topology rh" stage for almost 12hrs. How do I diagnosis the problem and fix it? I have attached the recon-all.log file. Thank you Best, Paul

3 13

negative header after preproc-sess
by Bai Haohao 01 Aug '17

01 Aug '17

Hello Freesurfer experts, I am running my data with preproc-sess to project my func data to individual anatomy file, and the command shows as below: preproc-sess -sf ${Sesslist} -fsd "bold" -surface self lhrh -fwhm 0 -per-run -force And the subjectname point to the subject dir that created after recon-all. After the running completed, I try to load data from fmcpr.sm0.self.lh.nii.gz with nibabel, and I get this error info: >>> f.get_data() Traceback (most recent call last): File "<stdin>", line 1, in <module> File "/usr/lib/pymodules/python2.7/nibabel/spatialimages.py", line 341, in get_data return np.asanyarray(self._data) File "/usr/lib/python2.7/dist-packages/numpy/core/numeric.py", line 512, in asanyarray return array(a, dtype, copy=False, order=order, subok=True) File "/usr/lib/pymodules/python2.7/nibabel/arrayproxy.py", line 55, in __array__ self._data = self._read_data() File "/usr/lib/pymodules/python2.7/nibabel/arrayproxy.py", line 60, in _read_data data = self.header.data_from_fileobj(fileobj) File "/usr/lib/pymodules/python2.7/nibabel/analyze.py", line 486, in data_from_fileobj data = self.raw_data_from_fileobj(fileobj) File "/usr/lib/pymodules/python2.7/nibabel/analyze.py", line 458, in raw_data_from_fileobj return array_from_file(shape, dtype, fileobj, offset) File "/usr/lib/pymodules/python2.7/nibabel/volumeutils.py", line 493, in array_from_file raise IOError(msg) IOError: Expected -1804 bytes, got 264809160 bytes from file "fmcpr.vol2surf.lh.nii.gz" - could the file be damaged? Then I check the file header by nibabel, and I get this: >>> print(f.get_header()) <class 'nibabel.nifti1.Nifti1Header'> object, endian='<' sizeof_hdr : 348 data_type : db_name : extents : 0 session_error : 0 regular : dim_info : 0 dim : [ 4 -1 1 1 451 1 1 1] intent_p1 : 0.0 intent_p2 : 0.0 intent_p3 : 0.0 intent_code : none datatype : float32 bitpix : 32 slice_start : 0 pixdim : [-1. 1. 1. 1. 2.00000072 1. 1. 1. ] vox_offset : 352.0 scl_slope : 0.0 scl_inter : 0.0 slice_end : 0 slice_code : unknown xyzt_units : 10 cal_max : 0.0 cal_min : 0.0 slice_duration : 0.0 toffset : 0.0 glmax : 0 glmin : 146790 descrip : FreeSurfer May 13 2013 aux_file : qform_code : scanner sform_code : scanner quatern_b : -0.0115927606821 quatern_c : -0.996071338654 quatern_d : -0.0864994972944 qoffset_x : 73344.5546875 qoffset_y : -1492.14978027 qoffset_z : -2311.28955078 srow_x : [ -9.99280393e-01 2.56918129e-02 2.79041883e-02 7.33445547e+04] srow_y : [ 2.04970520e-02 9.84766901e-01 -1.72667429e-01 -1.49214978e+03] srow_z : [ 3.19152586e-02 1.71971247e-01 9.84584868e-01 -2.31128955e+03] intent_name : magic : n+1 Note that the dim has value -1, but when I use -surface fsaverage, the dim is correct(show as below): dim : [ 4 27307 1 6 451 1 1 1] And I read the source code, the difference between self and fsaverage is appeared when running rawfunc2surf-sess, and log files are attached. I have tried many commands to load data from fmcpr.sm0.self.lh.nii.gz, such as fslview, freeview, mri_convert, mri_surf2surf, ... and only tksurfer could read this file by -timecourse fmcpr.sm0.self.lh.nii.gz. I want to figure out how could I fix it, and any suggestion would be helpful. Thanks in advance, Bai Haohao Version info: System: ubuntu-16.04.1-server-amd64 Freesurfer: freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0-HCP nibabel: python-nibabel 1.2.2-1

4 8

Volume based ROI projected to surface
by Sadie Marvel 01 Aug '17

01 Aug '17

Hi Freesurfers, I am doing a surfaced based ROI analysis on each of my subjects functional data. Using information from other papers, the size of the ROI really matters when doing the analysis, and I want to take this information from these papers and apply them to my own data. However, these papers use volume based ROI analysis, by making spheres that have 6 mm radiuses around the location of peak activity. To translate what they did to a surface based approach, I thought I would try to approximate how large this sphere would be if it were projected onto the surface of the brain by creating cubes around a certain location in the volume and projecting them to the surface using mri_vol2surf. That way, I would have approximately the same amount of information in my surface ROI. This is more of a general question, but I was wondering how this command actually works and whether it takes just one face or slice of the volume I created and projects that to the surface, or if it would project all 6 faces of the cube to the surface. And how is this volume actually translated into vertices? And how does the location of the cube in the volume space of the brain determine how large it will be on the surface? Do you have any suggestions as to how I can approach this problem better? Thanks?!

1 0

Cerebellum parcellation
by Otília 01 Aug '17

01 Aug '17

Hello, I would like to use the cerebellum atlas (http://www.freesurfer.net/fswiki/CerebellumParcellation_Buckner2011 [1]) to obtain parcellated cerebellum volumes. Is it possible? How? Thank you in advance, -- OTILIA Links: ------ [1] http://www.freesurfer.net/fswiki/CerebellumParcellation_Buckner2011

1 0

niiRead error
by Francesca Strappini 01 Aug '17

01 Aug '17

Hi, I'm trying to register to the surface a *t*-test map created with afni (3dttest++) but I got this error message: mri_vol2surf --mov movierestTest.nii.gz --regheader fsaverage --surf-fwhm 3 --hemi lh --o movierestTest_lh.nii.gz srcvol = movierestTest.nii.gz srcreg unspecified srcregold = 0 srcwarp unspecified surf = white hemi = lh reshape = 0 interp = nearest float2int = round GetProjMax = 0 INFO: float2int code = 0 niiRead(): 5 dimensions in /media/francesca/DATA/Shared/fmri-experiments/fc_categories/searchlight/tesrest/movierestTest.nii.gz; unsupported Invalid argument ERROR: could not read movierestTest.nii.gz as type 24 Thanks Francesca -- Francesca Strappini, Ph.D. Neurobiology Department Weizmann Institute of Science 234 Herzl Street, Rehovot 7610001 Israel Tel.: +972 58 444 2584 E-mail: francesca.strappini(a)weizmann.ac.il

3 5

Extracting vertex data from thickness maps after masking by sig.mgh
by Elijah Mak 01 Aug '17

01 Aug '17

Hi Freesurfer Team, I have previously used mri_binarize to derive the mask.mgh from the sig.mgh after a first-level group comparison of cortical thickness. Now, I would like to extract the vertex data from from another modality surface within and outside the mask in individual subjects. Is there an nice workflow to do that? Thanks a lot. I hope my question made sense! Best Wishes, Elijah

2 4

reducing a matrix
by Linda Eva Heidinger 31 Jul '17

31 Jul '17

Hello Dr. Greve, I ran the program below and got the following errors. Can you help??? I really would appreciate it. What does it mean?. -Linda ? Loading source LTA boldregister003.dat INFO: This REGISTER_DAT transform is valid only for volumes between COR types with c_(r,a,s) = 0. Loading GCAM Subject06/cvs_CVS35MNI152/final_CVSmorph_tocvs_avg35_inMNI152.m3z setting orig areas to linear transform determinant scaled 1.00 Loading destination LTA /pkg64/brainmap/freesurfer-v6.0.0_x86_64/subjects/cvs_avg35_inMNI152/mri.2mm/register.lta MRIvol2volGCAM(): VSM not used MRIvol2volGCAM(): interpolation type is 0 nearest MRIvol2volGCAM(): Chaning Source LTA type to vox2vox ? The initial command that was run: mri_vol2vol --gcam run_003regraijNIFTI.nii boldregister003.dat Subject06/cvs_CVS35MNI152/final_CVSmorph_tocvs_avg35_inMNI152.m3z $FREESURFER_HOME/subjects/cvs_avg35_inMNI152/mri.2mm/register.lta 0 0 subject003matrix.nii

1 0

reducing a matrix
by Linda Eva Heidinger 31 Jul '17

31 Jul '17

Hello Dr. Greve, I ran the program below and got the following errors. Can you help??? I really would appreciate it. What is wrong? -Linda ? Loading source LTA boldregister003.dat INFO: This REGISTER_DAT transform is valid only for volumes between COR types with c_(r,a,s) = 0. Loading GCAM Subject06/cvs_CVS35MNI152/final_CVSmorph_tocvs_avg35_inMNI152.m3z setting orig areas to linear transform determinant scaled 1.00 Loading destination LTA /pkg64/brainmap/freesurfer-v6.0.0_x86_64/subjects/cvs_avg35_inMNI152/mri.2mm/register.lta MRIvol2volGCAM(): VSM not used MRIvol2volGCAM(): interpolation type is 0 nearest MRIvol2volGCAM(): Chaning Source LTA type to vox2vox ? The initial command that was run: mri_vol2vol --gcam run_003regraijNIFTI.nii boldregister003.dat Subject06/cvs_CVS35MNI152/final_CVSmorph_tocvs_avg35_inMNI152.m3z $FREESURFER_HOME/subjects/cvs_avg35_inMNI152/mri.2mm/register.lta 0 0 subject003matrix.nii

1 0

creating mesh with specifications
by Yagmur Ozdemir 19 31 Jul '17

31 Jul '17

Hello freesurfer experts, I am trying to export an inflated surface file and its overlay made in Freesurfer to a different software and it seems like the surface file needs to have a particular number of vertices, triangles and average # of neighbors to be compatible. I have used mris_decimate and mris_apply_reg to simplify the files but the commands are not specific enough. Is there a way to use those commands in such a way or simply do recon-all with these specified qualities? Thank you for the help! Idil

2 2

Total White matter and CSF value Calculation
by M Janani 31 Jul '17

31 Jul '17

Hi Team, Could you please confirm whether the below mentioned formulas to compute Total WM and ventricular CSF are correct 1. Total White Matter = CerebralWhiteMatterVol + (lh+rh) Cerebellum White Matter 2. Total ventricular CSF = (lh + rh) Lateral-Ventricle + = (lh + rh)Inf-Lat-Vent + (lh + rh)choroid-plexus + 3rd-Ventricle + 4th-Ventricle Thanks for your support. Regards, Janani ::DISCLAIMER:: ---------------------------------------------------------------------------------------------------------------------------------------------------- The contents of this e-mail and any attachment(s) are confidential and intended for the named recipient(s) only. E-mail transmission is not guaranteed to be secure or error-free as information could be intercepted, corrupted, lost, destroyed, arrive late or incomplete, or may contain viruses in transmission. The e mail and its contents (with or without referred errors) shall therefore not attach any liability on the originator or HCL or its affiliates. Views or opinions, if any, presented in this email are solely those of the author and may not necessarily reflect the views or opinions of HCL or its affiliates. Any form of reproduction, dissemination, copying, disclosure, modification, distribution and / or publication of this message without the prior written consent of authorized representative of HCL is strictly prohibited. If you have received this email in error please delete it and notify the sender immediately. Before opening any email and/or attachments, please check them for viruses and other defects. ----------------------------------------------------------------------------------------------------------------------------------------------------

2 1

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