Freesurfer July 2019

freesurfer@nmr.mgh.harvard.edu

104 participants
165 discussions

View Results: Paired T-Test
by FAST Study 22 Jul '19

22 Jul '19

External Email - Use Caution Dear Dr. Greve, *Will you please help me learn how to view the output of the paired t-test - via mri_glmfit? I am new to FreeSurfer and trying to figure out what to load and where. How do we open the maps? What maps are best to open to view?* Thanks!

2 1

Using Freesurfer Commands for Neonate
by Mahshid Fouladivanda 21 Jul '19

21 Jul '19

External Email - Use Caution Dear Experts, I have a neonate MRI Image which its parcellation file, surface files and the ribbon are not created by freesurfer. I have created an annotation file for it using "write_annotation". Now, for further processing I need to use freesurfer commands like "mri_aparc2aseg". Now I have a general question. Can these commands be used for neonate images?? Regards, Mahshid

1 0

Failure of mri_robust_template in fmriprep
by Frederick, Blaise B. 21 Jul '19

21 Jul '19

Hi, I keep getting the same error every time I run fmriprep on subjects from the OASIS3 dataset. There are 5-7 T1 scans over 3-4 time points for most subjects, and the registration is failing every time with the return code -9. I can’t seem to find any indication of what that return code means, so I don’t know what to try to dix. Does anybody have an idea? Thanks, Blaise cat /n/scratch2/bdf1/OASIS/derivatives/fmriprep/sub-OAS30004/log/20190719-151129_2b54c614-de57-4bd6-9c95-9c721b09df7d/crash-20190719-153017-bdf1-t1_merge-59cde0ed-a554-4c50-8cc7-fd158f28f7ae.txt Node: fmriprep_wf.single_subject_OAS30004_wf.anat_preproc_wf.anat_template_wf.t1_merge Working directory: /n/scratch2/bdf1/OASIS/work/fmriprep_wf/single_subject_OAS30004_wf/anat_preproc_wf/anat_template_wf/t1_merge Node inputs: args = <undefined> auto_detect_sensitivity = True average_metric = <undefined> environ = {'SUBJECTS_DIR': '/home/bdf1/software/freesurfer/subjects', 'OMP_NUM_THREADS': '4'} fixed_timepoint = True in_files = ['/n/scratch2/bdf1/OASIS/work/fmriprep_wf/single_subject_OAS30004_wf/anat_preproc_wf/anat_template_wf/n4_correct/mapflow/_n4_correct0/sub-OAS30004_ses-d1101_run-01_T1w_corrected.nii.gz', '/n/scratch2/bdf1/OASIS/work/fmriprep_wf/single_subject_OAS30004_wf/anat_preproc_wf/anat_template_wf/n4_correct/mapflow/_n4_correct1/sub-OAS30004_ses-d1101_run-02_T1w_corrected.nii.gz', '/n/scratch2/bdf1/OASIS/work/fmriprep_wf/single_subject_OAS30004_wf/anat_preproc_wf/anat_template_wf/n4_correct/mapflow/_n4_correct2/sub-OAS30004_ses-d2229_run-01_T1w_corrected.nii.gz', '/n/scratch2/bdf1/OASIS/work/fmriprep_wf/single_subject_OAS30004_wf/anat_preproc_wf/anat_template_wf/n4_correct/mapflow/_n4_correct3/sub-OAS30004_ses-d2229_run-02_T1w_corrected.nii.gz', '/n/scratch2/bdf1/OASIS/work/fmriprep_wf/single_subject_OAS30004_wf/anat_preproc_wf/anat_template_wf/n4_correct/mapflow/_n4_correct4/sub-OAS30004_ses-d2232_run-01_T1w_ras_corrected.nii.gz', '/n/scratch2/bdf1/OASIS/work/fmriprep_wf/single_subject_OAS30004_wf/anat_preproc_wf/anat_template_wf/n4_correct/mapflow/_n4_correct5/sub-OAS30004_ses-d2232_run-02_T1w_corrected.nii.gz', '/n/scratch2/bdf1/OASIS/work/fmriprep_wf/single_subject_OAS30004_wf/anat_preproc_wf/anat_template_wf/n4_correct/mapflow/_n4_correct6/sub-OAS30004_ses-d3457_T1w_ras_corrected.nii.gz'] in_intensity_scales = <undefined> initial_timepoint = 1 initial_transforms = <undefined> intensity_scaling = True no_iteration = True num_threads = 7 out_file = sub-OAS30004_ses-d1101_run-01_T1w_template.nii.gz outlier_sensitivity = <undefined> scaled_intensity_outputs = <undefined> subjects_dir = /home/bdf1/software/freesurfer/subjects subsample_threshold = 200 transform_outputs = True Traceback (most recent call last): File "/home/bdf1/software/anaconda3/envs/fmriprep141sing/lib/python3.7/site-packages/nipype/pipeline/plugins/multiproc.py", line 69, in run_node result['result'] = node.run(updatehash=updatehash) File "/home/bdf1/software/anaconda3/envs/fmriprep141sing/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py", line 472, in run result = self._run_interface(execute=True) File "/home/bdf1/software/anaconda3/envs/fmriprep141sing/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py", line 563, in _run_interface return self._run_command(execute) File "/home/bdf1/software/anaconda3/envs/fmriprep141sing/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py", line 643, in _run_command result = self._interface.run(cwd=outdir) File "/home/bdf1/software/anaconda3/envs/fmriprep141sing/lib/python3.7/site-packages/nipype/interfaces/freesurfer/base.py", line 265, in run return super(FSCommandOpenMP, self).run(**inputs) File "/home/bdf1/software/anaconda3/envs/fmriprep141sing/lib/python3.7/site-packages/nipype/interfaces/freesurfer/base.py", line 144, in run return super(FSCommand, self).run(**inputs) File "/home/bdf1/software/anaconda3/envs/fmriprep141sing/lib/python3.7/site-packages/nipype/interfaces/base/core.py", line 375, in run runtime = self._run_interface(runtime) File "/home/bdf1/software/anaconda3/envs/fmriprep141sing/lib/python3.7/site-packages/nipype/interfaces/base/core.py", line 758, in _run_interface self.raise_exception(runtime) File "/home/bdf1/software/anaconda3/envs/fmriprep141sing/lib/python3.7/site-packages/nipype/interfaces/base/core.py", line 695, in raise_exception ).format(**runtime.dictcopy())) RuntimeError: Command: mri_robust_template --satit --fixtp --mov /n/scratch2/bdf1/OASIS/work/fmriprep_wf/single_subject_OAS30004_wf/anat_preproc_wf/anat_template_wf/n4_correct/mapflow/_n4_correct0/sub-OAS30004_ses-d1101_run-01_T1w_corrected.nii.gz /n/scratch2/bdf1/OASIS/work/fmriprep_wf/single_subject_OAS30004_wf/anat_preproc_wf/anat_template_wf/n4_correct/mapflow/_n4_correct1/sub-OAS30004_ses-d1101_run-02_T1w_corrected.nii.gz /n/scratch2/bdf1/OASIS/work/fmriprep_wf/single_subject_OAS30004_wf/anat_preproc_wf/anat_template_wf/n4_correct/mapflow/_n4_correct2/sub-OAS30004_ses-d2229_run-01_T1w_corrected.nii.gz /n/scratch2/bdf1/OASIS/work/fmriprep_wf/single_subject_OAS30004_wf/anat_preproc_wf/anat_template_wf/n4_correct/mapflow/_n4_correct3/sub-OAS30004_ses-d2229_run-02_T1w_corrected.nii.gz /n/scratch2/bdf1/OASIS/work/fmriprep_wf/single_subject_OAS30004_wf/anat_preproc_wf/anat_template_wf/n4_correct/mapflow/_n4_correct4/sub-OAS30004_ses-d2232_run-01_T1w_ras_corrected.nii.gz /n/scratch2/bdf1/OASIS/work/fmriprep_wf/single_subject_OAS30004_wf/anat_preproc_wf/anat_template_wf/n4_correct/mapflow/_n4_correct5/sub-OAS30004_ses-d2232_run-02_T1w_corrected.nii.gz /n/scratch2/bdf1/OASIS/work/fmriprep_wf/single_subject_OAS30004_wf/anat_preproc_wf/anat_template_wf/n4_correct/mapflow/_n4_correct6/sub-OAS30004_ses-d3457_T1w_ras_corrected.nii.gz --inittp 1 --iscale --noit --template sub-OAS30004_ses-d1101_run-01_T1w_template.nii.gz --subsample 200 --lta /n/scratch2/bdf1/OASIS/work/fmriprep_wf/single_subject_OAS30004_wf/anat_preproc_wf/anat_template_wf/t1_merge/tp1.lta /n/scratch2/bdf1/OASIS/work/fmriprep_wf/single_subject_OAS30004_wf/anat_preproc_wf/anat_template_wf/t1_merge/tp2.lta /n/scratch2/bdf1/OASIS/work/fmriprep_wf/single_subject_OAS30004_wf/anat_preproc_wf/anat_template_wf/t1_merge/tp3.lta /n/scratch2/bdf1/OASIS/work/fmriprep_wf/single_subject_OAS30004_wf/anat_preproc_wf/anat_template_wf/t1_merge/tp4.lta /n/scratch2/bdf1/OASIS/work/fmriprep_wf/single_subject_OAS30004_wf/anat_preproc_wf/anat_template_wf/t1_merge/tp5.lta /n/scratch2/bdf1/OASIS/work/fmriprep_wf/single_subject_OAS30004_wf/anat_preproc_wf/anat_template_wf/t1_merge/tp6.lta /n/scratch2/bdf1/OASIS/work/fmriprep_wf/single_subject_OAS30004_wf/anat_preproc_wf/anat_template_wf/t1_merge/tp7.lta Standard output: $Id: mri_robust_template.cpp,v 1.54 2016/05/05 21:17:08 mreuter Exp $ --satit: Will estimate SAT iteratively! --fixtp: Will map everything to init TP! --mov: Using /n/scratch2/bdf1/OASIS/work/fmriprep_wf/single_subject_OAS30004_wf/anat_preproc_wf/anat_template_wf/n4_correct/mapflow/_n4_correct0/sub-OAS30004_ses-d1101_run-01_T1w_corrected.nii.gz as movable/source volume. --mov: Using /n/scratch2/bdf1/OASIS/work/fmriprep_wf/single_subject_OAS30004_wf/anat_preproc_wf/anat_template_wf/n4_correct/mapflow/_n4_correct1/sub-OAS30004_ses-d1101_run-02_T1w_corrected.nii.gz as movable/source volume. --mov: Using /n/scratch2/bdf1/OASIS/work/fmriprep_wf/single_subject_OAS30004_wf/anat_preproc_wf/anat_template_wf/n4_correct/mapflow/_n4_correct2/sub-OAS30004_ses-d2229_run-01_T1w_corrected.nii.gz as movable/source volume. --mov: Using /n/scratch2/bdf1/OASIS/work/fmriprep_wf/single_subject_OAS30004_wf/anat_preproc_wf/anat_template_wf/n4_correct/mapflow/_n4_correct3/sub-OAS30004_ses-d2229_run-02_T1w_corrected.nii.gz as movable/source volume. --mov: Using /n/scratch2/bdf1/OASIS/work/fmriprep_wf/single_subject_OAS30004_wf/anat_preproc_wf/anat_template_wf/n4_correct/mapflow/_n4_correct4/sub-OAS30004_ses-d2232_run-01_T1w_ras_corrected.nii.gz as movable/source volume. --mov: Using /n/scratch2/bdf1/OASIS/work/fmriprep_wf/single_subject_OAS30004_wf/anat_preproc_wf/anat_template_wf/n4_correct/mapflow/_n4_correct5/sub-OAS30004_ses-d2232_run-02_T1w_corrected.nii.gz as movable/source volume. --mov: Using /n/scratch2/bdf1/OASIS/work/fmriprep_wf/single_subject_OAS30004_wf/anat_preproc_wf/anat_template_wf/n4_correct/mapflow/_n4_correct6/sub-OAS30004_ses-d3457_T1w_ras_corrected.nii.gz as movable/source volume. Total: 7 input volumes --inittp: Using TP 1 as target for initialization --iscale: Enableing intensity scaling! --noit: Will output only first template (no iterations)! --template: Using sub-OAS30004_ses-d1101_run-01_T1w_template.nii.gz as template output volume. --subsample: Will subsample if size is larger than 200 on all axes! --lta: Will output LTA transforms Setting iscale ... reading source '/n/scratch2/bdf1/OASIS/work/fmriprep_wf/single_subject_OAS30004_wf/anat_preproc_wf/anat_template_wf/n4_correct/mapflow/_n4_correct0/sub-OAS30004_ses-d1101_run-01_T1w_corrected.nii.gz'... converting source '/n/scratch2/bdf1/OASIS/work/fmriprep_wf/single_subject_OAS30004_wf/anat_preproc_wf/anat_template_wf/n4_correct/mapflow/_n4_correct0/sub-OAS30004_ses-d1101_run-01_T1w_corrected.nii.gz' to bspline ... MRItoBSpline degree 3 reading source '/n/scratch2/bdf1/OASIS/work/fmriprep_wf/single_subject_OAS30004_wf/anat_preproc_wf/anat_template_wf/n4_correct/mapflow/_n4_correct1/sub-OAS30004_ses-d1101_run-02_T1w_corrected.nii.gz'... converting source '/n/scratch2/bdf1/OASIS/work/fmriprep_wf/single_subject_OAS30004_wf/anat_preproc_wf/anat_template_wf/n4_correct/mapflow/_n4_correct1/sub-OAS30004_ses-d1101_run-02_T1w_corrected.nii.gz' to bspline ... MRItoBSpline degree 3 reading source '/n/scratch2/bdf1/OASIS/work/fmriprep_wf/single_subject_OAS30004_wf/anat_preproc_wf/anat_template_wf/n4_correct/mapflow/_n4_correct2/sub-OAS30004_ses-d2229_run-01_T1w_corrected.nii.gz'... converting source '/n/scratch2/bdf1/OASIS/work/fmriprep_wf/single_subject_OAS30004_wf/anat_preproc_wf/anat_template_wf/n4_correct/mapflow/_n4_correct2/sub-OAS30004_ses-d2229_run-01_T1w_corrected.nii.gz' to bspline ... MRItoBSpline degree 3 reading source '/n/scratch2/bdf1/OASIS/work/fmriprep_wf/single_subject_OAS30004_wf/anat_preproc_wf/anat_template_wf/n4_correct/mapflow/_n4_correct3/sub-OAS30004_ses-d2229_run-02_T1w_corrected.nii.gz'... converting source '/n/scratch2/bdf1/OASIS/work/fmriprep_wf/single_subject_OAS30004_wf/anat_preproc_wf/anat_template_wf/n4_correct/mapflow/_n4_correct3/sub-OAS30004_ses-d2229_run-02_T1w_corrected.nii.gz' to bspline ... MRItoBSpline degree 3 reading source '/n/scratch2/bdf1/OASIS/work/fmriprep_wf/single_subject_OAS30004_wf/anat_preproc_wf/anat_template_wf/n4_correct/mapflow/_n4_correct4/sub-OAS30004_ses-d2232_run-01_T1w_ras_corrected.nii.gz'... converting source '/n/scratch2/bdf1/OASIS/work/fmriprep_wf/single_subject_OAS30004_wf/anat_preproc_wf/anat_template_wf/n4_correct/mapflow/_n4_correct4/sub-OAS30004_ses-d2232_run-01_T1w_ras_corrected.nii.gz' to bspline ... MRItoBSpline degree 3 reading source '/n/scratch2/bdf1/OASIS/work/fmriprep_wf/single_subject_OAS30004_wf/anat_preproc_wf/anat_template_wf/n4_correct/mapflow/_n4_correct5/sub-OAS30004_ses-d2232_run-02_T1w_corrected.nii.gz'... converting source '/n/scratch2/bdf1/OASIS/work/fmriprep_wf/single_subject_OAS30004_wf/anat_preproc_wf/anat_template_wf/n4_correct/mapflow/_n4_correct5/sub-OAS30004_ses-d2232_run-02_T1w_corrected.nii.gz' to bspline ... MRItoBSpline degree 3 reading source '/n/scratch2/bdf1/OASIS/work/fmriprep_wf/single_subject_OAS30004_wf/anat_preproc_wf/anat_template_wf/n4_correct/mapflow/_n4_correct6/sub-OAS30004_ses-d3457_T1w_ras_corrected.nii.gz'... converting source '/n/scratch2/bdf1/OASIS/work/fmriprep_wf/single_subject_OAS30004_wf/anat_preproc_wf/anat_template_wf/n4_correct/mapflow/_n4_correct6/sub-OAS30004_ses-d3457_T1w_ras_corrected.nii.gz' to bspline ... MRItoBSpline degree 3 MultiRegistration::initializing Xforms (init 1 , maxres 0 , iterate 5 , epsit 0.01 ) : [init] ========================= TP 5 to TP 1 ============================== Register TP 5 ( /n/scratch2/bdf1/OASIS/work/fmriprep_wf/single_subject_OAS30004_wf/anat_preproc_wf/anat_template_wf/n4_correct/mapflow/_n4_correct4/sub-OAS30004_ses-d2232_run-01_T1w_ras_corrected.nii.gz ) to TP 1 ( /n/scratch2/bdf1/OASIS/work/fmriprep_wf/single_subject_OAS30004_wf/anat_preproc_wf/anat_template_wf/n4_correct/mapflow/_n4_correct0/sub-OAS30004_ses-d1101_run-01_T1w_corrected.nii.gz ) [init] ========================= TP 6 to TP 1 ============================== Register TP 6 ( /n/scratch2/bdf1/OASIS/work/fmriprep_wf/single_subject_OAS30004_wf/anat_preproc_wf/anat_template_wf/n4_correct/mapflow/_n4_correct5/sub-OAS30004_ses-d2232_run-02_T1w_corrected.nii.gz ) to TP 1 ( /n/scratch2/bdf1/OASIS/work/fmriprep_wf/single_subject_OAS30004_wf/anat_preproc_wf/anat_template_wf/n4_correct/mapflow/_n4_correct0/sub-OAS30004_ses-d1101_run-01_T1w_corrected.nii.gz ) [init] ========================= TP 3 to TP 1 ============================== Register TP 3 ( /n/scratch2/bdf1/OASIS/work/fmriprep_wf/single_subject_OAS30004_wf/anat_preproc_wf/anat_template_wf/n4_correct/mapflow/_n4_correct2/sub-OAS30004_ses-d2229_run-01_T1w_corrected.nii.gz ) to TP 1 ( /n/scratch2/bdf1/OASIS/work/fmriprep_wf/single_subject_OAS30004_wf/anat_preproc_wf/anat_template_wf/n4_correct/mapflow/_n4_correct0/sub-OAS30004_ses-d1101_run-01_T1w_corrected.nii.gz ) [init] ========================= TP 4 to TP 1 ============================== Register TP 4 ( /n/scratch2/bdf1/OASIS/work/fmriprep_wf/single_subject_OAS30004_wf/anat_preproc_wf/anat_template_wf/n4_correct/mapflow/_n4_correct3/sub-OAS30004_ses-d2229_run-02_T1w_corrected.nii.gz ) to TP 1 ( /n/scratch2/bdf1/OASIS/work/fmriprep_wf/single_subject_OAS30004_wf/anat_preproc_wf/anat_template_wf/n4_correct/mapflow/_n4_correct0/sub-OAS30004_ses-d1101_run-01_T1w_corrected.nii.gz ) [init] ========================= TP 7 to TP 1 ============================== Register TP 7 ( /n/scratch2/bdf1/OASIS/work/fmriprep_wf/single_subject_OAS30004_wf/anat_preproc_wf/anat_template_wf/n4_correct/mapflow/_n4_correct6/sub-OAS30004_ses-d3457_T1w_ras_corrected.nii.gz ) to TP 1 ( /n/scratch2/bdf1/OASIS/work/fmriprep_wf/single_subject_OAS30004_wf/anat_preproc_wf/anat_template_wf/n4_correct/mapflow/_n4_correct0/sub-OAS30004_ses-d1101_run-01_T1w_corrected.nii.gz ) [init] ========================= TP 2 to TP 1 ============================== Register TP 2 ( /n/scratch2/bdf1/OASIS/work/fmriprep_wf/single_subject_OAS30004_wf/anat_preproc_wf/anat_template_wf/n4_correct/mapflow/_n4_correct1/sub-OAS30004_ses-d1101_run-02_T1w_corrected.nii.gz ) to TP 1 ( /n/scratch2/bdf1/OASIS/work/fmriprep_wf/single_subject_OAS30004_wf/anat_preproc_wf/anat_template_wf/n4_correct/mapflow/_n4_correct0/sub-OAS30004_ses-d1101_run-01_T1w_corrected.nii.gz ) -- Original : (0.999994, 1, 1)mm and (176, 256, 256) voxels. -- Resampled: (0.999996, 0.999996, 0.999996)mm and (176, 257, 257) voxels. -- Reslicing using cubic bspline -- Original : (1, 1, 1)mm and (176, 256, 256) voxels. -- Resampled: (1, 1, 1)mm and (177, 256, 256) voxels. -- Reslicing using cubic bspline -- Original : (0.999994, 1, 1)mm and (176, 256, 256) voxels. -- Resampled: (0.999996, 0.999996, 0.999996)mm and (176, 257, 257) voxels. -- Reslicing using cubic bspline -- Original : (1, 1, 1)mm and (176, 256, 256) voxels. -- Resampled: (1, 1, 1)mm and (177, 256, 256) voxels. -- Reslicing using cubic bspline -- Original : (0.999994, 1, 1)mm and (176, 256, 256) voxels. -- Resampled: (0.999996, 0.999996, 0.999996)mm and (176, 257, 257) voxels. -- Reslicing using cubic bspline -- Original : (0.999994, 1, 1)mm and (176, 256, 256) voxels. -- Resampled: (0.999996, 0.999996, 0.999996)mm and (176, 257, 257) voxels. -- Reslicing using cubic bspline MRItoBSpline degree 3 MRItoBSpline degree 3 MRItoBSpline degree 3 MRItoBSpline degree 3 MRItoBSpline degree 3 MRItoBSpline degree 3 -- Original : (0.999996, 1, 1)mm and (176, 256, 256) voxels. -- Resampled: (1, 1, 1)mm and (177, 256, 256) voxels. -- Reslicing using cubic bspline MRItoBSpline degree 3 -- Original : (0.999996, 1, 1)mm and (176, 256, 256) voxels. -- Resampled: (0.999996, 0.999996, 0.999996)mm and (176, 257, 257) voxels. -- Reslicing using cubic bspline MRItoBSpline degree 3 -- Original : (0.999996, 1, 1)mm and (176, 256, 256) voxels. -- Resampled: (0.999996, 0.999996, 0.999996)mm and (176, 257, 257) voxels. -- Reslicing using cubic bspline MRItoBSpline degree 3 -- Original : (0.999996, 1, 1)mm and (176, 256, 256) voxels. -- Resampled: (0.999996, 0.999996, 0.999996)mm and (176, 257, 257) voxels. -- Reslicing using cubic bspline MRItoBSpline degree 3 -- Original : (0.999996, 1, 1)mm and (176, 256, 256) voxels. -- Resampled: (0.999996, 0.999996, 0.999996)mm and (176, 257, 257) voxels. -- Reslicing using cubic bspline -- Original : (0.999996, 1, 1)mm and (176, 256, 256) voxels. -- Resampled: (1, 1, 1)mm and (177, 256, 256) voxels. -- Reslicing using cubic bspline MRItoBSpline degree 3 MRItoBSpline degree 3 - Max Resolution used: 2 -- gpS ( 44 , 64 , 64 ) -- gpT ( 44 , 64 , 64 ) - running loop to estimate saturation parameter: - Max Resolution used: 2 -- gpS ( 44 , 64 , 64 ) -- gpT ( 44 , 64 , 64 ) - running loop to estimate saturation parameter: - Max Resolution used: 2 -- gpS ( 44 , 64 , 64 ) -- gpT ( 44 , 64 , 64 ) - running loop to estimate saturation parameter: - Max Resolution used: 2 -- gpS ( 44 , 64 , 64 ) -- gpT ( 44 , 64 , 64 ) - running loop to estimate saturation parameter: - Max Resolution used: 2 -- gpS ( 44 , 64 , 64 ) -- gpT ( 44 , 64 , 64 ) - running loop to estimate saturation parameter: - Max Resolution used: 2 -- gpS ( 44 , 64 , 64 ) -- gpT ( 44 , 64 , 64 ) Standard error: Return code: -9 ------------------------------------------------------- Blaise Frederick Associate Professor of Psychiatry/Biophysicist Harvard Medical School/McLean Hospital bbfrederick(a)mclean.harvard.edu http://www.nirs-fmri.net

2 1

mais_ca_label
by Valentina Mancini 19 Jul '19

19 Jul '19

External Email - Use Caution Dear Freesurfer experts, we are trying to use your function "mris_ca_label" in order to get an annotation file in the subject's space using the Schaefer-Yeo atlas. However, we noticed that a "special classifier array" is required among the inputs. Could you pleas give us more information about the type of file required and where we can find it? Thank you and best regards, Valentina Mancini

3 3

QDEC interpretation question - Please respond
by Avi Gharehgazlou 19 Jul '19

19 Jul '19

External Email - Use Caution Hi, I have a question regarding interpreting results from QDEC. I am investigating lGI in individuals with ASD and controls (which I will refer to as 'TD' here). I understand from the archives that when "TD" is listed first and "ASD" is listed second in my "diagnosis.levels" file, when I select the question "Does average lGI, accounting for sex, differ between TD and ASD?" results would be interpreted as: Yellow regions = greater lGI in TD; blue regions = reduced lGI in TD. Assuming the same order, I thought that since I listed "females" first and "males" second on my "sex.levels" file, then results from selecting question "Does average lGI, accounting for diagnosis, differ between females and males?" would be interpreted as: Yellow regions= greater lGI in females; blue regions = reduced lGI in females. Is this correct? The reason I'm asking is that when I extract mean lGI values of significant clusters (between females and males in the latter case above) and plot the mean lGIs for males and females separately, I see that the yellow regions show greater lGI in males instead of females! Will you please clarify for me how I have to interpret these results Thanks so much Avi

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Patient vs group of controls
by m s 18 Jul '19

18 Jul '19

External Email - Use Caution Hello Freesurfer experts! I need to compare one patient to a group of controls and I wanted to know which is the best way to do this. Is it correct to do it with group analysis when 1 group only has one patient, thus no stdev, and the other group (controls) has for ex 20 patients? Is there a better choice for this situation or a prefered way to visualize result in this case?? Thank you! Mercedes

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Re: [Freesurfer] Command line tksurfer: use of the color scale "Color Wheel"
by Greve, Douglas N.,Ph.D. 18 Jul '19

18 Jul '19

In freeview, you can use :overlay_color=colorscale,settings maybe Ruopeng can weigh in on exactly what to set them to to get the colorwheel Are you also looking to have freeview snap pictures for you? On 7/18/19 11:57 AM, Matthieu VANHOUTTE wrote: > External Email - Use Caution > Sorry not to be precise on my answer. > > I can easily open freeview to load overlay on surface and configure > the color scale to "Color Wheel". > > However to create pictur es for article I automatize the creation > of those pictures by scripting using tksurfer command line. There are > different options for this command line but I didn't find any option > to set the color scale to which I want "Color Wheel". > > Is there any tool existing allowing to use "Color Wheel" color scale > by scripting ? > > Best, > > Matthieu > > On 18/07/2019 17:51, Greve, Douglas N.,Ph.D. wrote: >> I don't know what you mean by "stay graphical". can you explain? What is >> the tksurfer option to load the colorwheel? >> >> On 7/18/19 11:47 AM, Matthieu VANHOUTTE wrote: >>> External Email - Use Caution >>> Hi Douglas, Bruce, >>> >>> Freeview is really nice but stay graphical. When I want to create >>> composed snapshots of surface overlays I use tksurfer with command >>> lines to create these. >>> >>> I looked at tksurferfv with command lines but didn't see where is the >>> option to set color scale to "Color Wheel"? >>> >>> Best, >>> >>> Matthieu >>> >>> On 18/07/2019 17:22, Greve, Douglas N.,Ph.D. wrote: >>>> There is a program called tksurferfv that runs freeview but takes all >>>> the same command line args as tksurfer >>>> >>>> On 7/18/19 10:56 AM, Bruce Fischl wrote: >>>>> Hi Matthieu >>>>> >>>>> tksurfer has been deprecated for years. Is there a reason you can't >>>>> switch to freeview? >>>>> >>>>> cheers >>>>> Bruce >>>>> On Thu, 18 Jul 2019, Matthieu VANHOUTTE wrote: >>>>> >>>>>> External Email - Use Caution >>>>>> >>>>>> Dear experts, >>>>>> >>>>>> I use tksurfer in command line to generate multiple faces images of >>>>>> overlays on the fsaverage surface. >>>>>> >>>>>> Graphically it is possible via freeview to set the color scale of >>>>>> the >>>>>> overlay with "Color Wheel" setting. I searched into the tksufer >>>>>> command >>>>>> help but didn' t find any option to specify this color scale. Doas >>>>>> anyone know how to deal with it by command lines ? >>>>>> >>>>>> Best regards, >>>>>> >>>>>> Matthieu >>>>>> >>>>>> >>>>>> _______________________________________________ >>>>>> Freesurfer mailing list >>>>>> Freesurfer(a)nmr.mgh.harvard.edu >>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>>> >>>>>> >>>>>> >>>>> _______________________________________________ >>>>> Freesurfer mailing list >>>>> Freesurfer(a)nmr.mgh.harvard.edu >>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>> _______________________________________________ >>>> 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.

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voxel coordinates of corpus collosum
by Sadia Sheikh 18 Jul '19

18 Jul '19

External Email - Use Caution Dear Freesurfer experts How can I get the voxel coordinates of the segmented corpus callosum? I tried using the command mri_vol2label and id of the corpus callosum as 192 as given in Freesurfer LUT, but it gives an error: found no voxels matching id 192 Thanks in advance Sadia

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How to make a SlicDelayFile in FSFAST
by Zhi Li 18 Jul '19

18 Jul '19

External Email - Use Caution Dear Freesurfer experts, May I ask how to create a slice delay file for slice timing in fsfast? Is there an example? The slice order of my data is [33:-2:1 32:-2:2], how could I convert this vector to time fraction of TR? I have checked the help information of slicetimer of FSL, but it is unclear to me and I did not found an example of it. Any suggestions? Thanks and best regards, LIzhi

1 0

Command line tksurfer: use of the color scale "Color Wheel"
by Matthieu VANHOUTTE 18 Jul '19

18 Jul '19

External Email - Use Caution Dear experts, I use tksurfer in command line to generate multiple faces images of overlays on the fsaverage surface. Graphically it is possible via freeview to set the color scale of the overlay with "Color Wheel" setting. I searched into the tksufer command help but didn' t find any option to specify this color scale. Doas anyone know how to deal with it by command lines ? Best regards, Matthieu

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Freesurfer July 2019