Freesurfer June 2017

freesurfer@nmr.mgh.harvard.edu

116 participants
186 discussions

Medial Surface Problem
by Bronwyn Overs 03 Aug '17

03 Aug '17

Hi mailing list, I am currently processing a longitudinal image and have come across a problem at the medial surface in the long image (step 3). As you can see in the attached image, the rh medial surface has been significantly overestimated and extends into the lh surface. This error showed up only in only 1 of the 2 long images for this subject, and both the time-point images and the base are perfectly fine. Do you know why this is happening? Kind regards, Bronwyn Overs Research Assistant Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia M 0411 308 769 T +61 2 9399 1883 F +61 2 9399 1265 neura.edu.au <http://neura.edu.au/> <https://twitter.com/neuraustralia> <https://www.facebook.com/NeuroscienceResearchAustralia> <http://www.neura.edu.au/help-research/subscribe>

4 19

output with input matrix size and referential
by pierre deman 02 Aug '17

02 Aug '17

Hello, I am trying to have the atlases aparc.a2009+aseg.mgz, hippocampal subfield etc ... in a matrix with the same size as the input of recon-all (and not the cubic matrix 256x256x256) and with the same orientation. what is the best way to do it ? Cheers, Pierre -- DEMAN Pierre Mobile : +33 7 82 57 80 94

4 3

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

RBV PVC: Saving output file before upsampling
by SudEEpti 18 Jul '17

18 Jul '17

Hello, Is there a way to save the PVC (RBV) output in native PET resolution, before upsampling? Would you also be able to share the command that is used for upsampling? I would like to play with a different type of interpolation. Thank you very much. Su

3 5

Subject with missing fMRI data
by Sadie Marvel 12 Jul '17

12 Jul '17

Hi List, I am currently doing a group analysis of 26 subjects, one of which has missing fMRI data where the signal cuts off through parts of the occipital and temporal lobes. I was wondering if freesurfer has any way of dealing with this, such as multiple imputation, or other methods of filling the missing data. Alternatively, is there a way to only use the portions of the brain that have data when doing mri_glmfit? Does freesurfer do this automatically? Thanks.

3 10

Pial surface editing
by Michelle VanTieghem 12 Jul '17

12 Jul '17

Hello, We have assessed freesurfer output for 160+ brains, and about 50% have poor segmentation of pial matter that includes too much skull. Manual edits and re-running does work to improve the problem, but is very time/labor intensive for so many scans. I saw on the freesurfer wiki that you can include T2 or Flair images to improve the segmentation for this problem. However, we do not have these extra scans. What do you recommend to do otherwise? Thank you! -- Michelle VanTieghem PhD student in Psychology Developmental Affective Neuroscience Lab Columbia University mrv2115(a)columbia.edu

2 9

Qdec error in analysis
by AYUSHI SHUKLA 12 Jul '17

12 Jul '17

Hi, I'm a new user of qdec and I'm trying to run a cortical thickness analysis in qdec between Schizophrenic patients and healthy controls. I have run "recon-all -i" and "recon-all -s <subjid> -qcache" on my data and it says that this has run successfully without any errors. But when I hit analyze on the qdec GUI, I get the following error- "Error in Analyze: Couldn't open /Applications/freesurfer/subjects/5/surf/lh.thickness.fwhm10.fsaverage.mgz or .mgh file." I went through the old questions with the same issue, however I could not figure a solution for my problem as when I check in the directory, the file is present. I have tried to re-run recon-all and recon-all -s as well, but it is still giving the same error. I was wondering if someone could help me with this issue. Warm Regards Ayushi Shukla

3 3

viewing mri_glmfit FDR corrected results
by marco mcsweeney 11 Jul '17

11 Jul '17

Dear FreeSurfer experts, I ran my group analysis using mri_glmfit and found a number of significant clusters showing cortical thickness differences between 2 groups. I used tksurfer to visualize the results and used FDR to correct for multiple comparisons. My question is about how do I correctly get the FDR corrected results showing cluster number, size, MNI coordinates etc. as I would if I used QDEC? I have searched through the archives and have found what looks like the answer, but I'm not convinced that the method I used is correct. I used 1) mri_glmfit-sim --glmdir lh.group_diff.glmdir --cache 1.3 abs --cwpvalthresh .99 and 2) less lh.group_diff.glmdir/contrast.txt/cache.th13.abs.sig.cluster.summary However when I visualize the FDR corrected results with tksurfer or freeview I can see a couple of clusters not listed in the summary. Am I missing something? Thank you so much in advance. Any help or advice would be greatly appreciated. Best wishes Marco

2 2

surface inaccuracies around the optic chiasm
by Gabor Perlaki 09 Jul '17

09 Jul '17

Dear all, I use Freesurfer 6. In some of my subjects the surfaces (both pial and white) intruding into the optic chiasm. However, when I check the aparc.DKTatlas+aseg.mgz it seems that although the surfaces are wrong, the region is segmented as optic chiasm. Can I ignore this type of surface inaccuracies similarly to surface inacurracies around the amygdala and hippocampus? Best Regards, Gabor

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Freesurfer June 2017