Freesurfer

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30132 discussions

How would one run N4 bias corrected T1 and T2 images through FreeSurfer v6.0
by Axelson, Eric D 16 Feb '18

16 Feb '18

We are using N4 to correct some large inhomogeneities in some samples and wanted to insert these images into the v6.0 pipeline and bypass the N3 bias correction done within. What would be the correct sequence of freesurfer commands to achieve this? Thanks Eric ________________________________ Notice: This UI Health Care e-mail (including attachments) is covered by the Electronic Communications Privacy Act, 18 U.S.C. 2510-2521 and is intended only for the use of the individual or entity to which it is addressed, and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If you are not the intended recipient, any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please notify the sender immediately and delete or destroy all copies of the original message and attachments thereto. Email sent to or from UI Health Care may be retained as required by law or regulation. Thank you. ________________________________

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Re: [Freesurfer] IndexError: list index out of range
by Maksimovskiy, Arkadiy 16 Feb '18

16 Feb '18

Hi Doug, I sent you the tar files, but just wanted to update you that I tried running this with just one subjects and am still getting an error but a different one. The two inputs and output errors in the terminal are pasted below: [arkadiysimac:Freesurfer/Freesurfer_Files_with_Freesurfer_Masks/Post_Manual_Edits] amaksimovskiy% asegstats2table --subjects SILVA030 --meas volume --stats aseg.stats --tablefile Subcortical_GM_Volume1.Dec17.txt SUBJECTS_DIR : /Volumes/silverilab/Arkadiy/Freesurfer/Freesurfer_Files_with_Freesurfer_Masks/Post_Manual_Edits Parsing the .stats files Traceback (most recent call last): File "/Applications/freesurfer/bin/asegstats2table", line 548, in <module> id_name_map, measurelist = parsed.parse(options.meas) File "/Applications/freesurfer/bin/fsutils.py", line 115, in parse seg = strlst[1] # segmentation id is in the 2nd field IndexError: list index out of range [arkadiysimac:Freesurfer/Freesurfer_Files_with_Freesurfer_Masks/Post_Manual_Edits] amaksimovskiy% asegstats2table --subjects SILVA040 --meas volume --stats aseg.stats --tablefile Subcortical_GM_Volume1.Dec17.txt SUBJECTS_DIR : /Volumes/silverilab/Arkadiy/Freesurfer/Freesurfer_Files_with_Freesurfer_Masks/Post_Manual_Edits Parsing the .stats files Traceback (most recent call last): File "/Applications/freesurfer/bin/asegstats2table", line 548, in <module> id_name_map, measurelist = parsed.parse(options.meas) File "/Applications/freesurfer/bin/fsutils.py", line 122, in parse self.measurelist.append( float(strlst[self.measure_column_map[measure]] )) ValueError: could not convert string to float: Left-Cerebellum-Cortex Let me know if any further info is needed to troubleshoot. Thank you for helping with this. -arkadiy -- Arkadiy L. Maksimovskiy, Ph.D. Postdoctoral Research Fellow McLean Imaging Center, McLean Hospital Department of Psychiatry, Harvard Medical School

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List needed: pathway <==> freesurfer ROI
by Krieger, Donald N. 16 Feb '18

16 Feb '18

Dear List, I need a list of Freesurfer ROIs which are typical endpoints for each standard pathway used in tracula. I think this information is likely included in the default tracula atlas which I have been unable to find although I do not need spatial coordinates but rather just the list of ROI names for each pathway. If this information is contained in publications, I would like to cite them. I hope this is clear and thank you for any help you can provide. Best - Don Don Krieger, Ph.D. Research Scientist Department of Neurological Surgery University of Pittsburgh

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aparcstats2table subject space?
by Kasper Jessen 15 Feb '18

15 Feb '18

Dear FreeSurfer, When you extract e.g. thickness from the command aparcstats2table - is the data extracted from subject space? We need to know whether or not, we need to covariate for total brain volume. Bw Kasper Kasper Jessen, MD, PhD student Center for Neuropsychiatric Schizophrenia Research (CNSR) Mental Health Centre Glostrup Nordre Ringvej 29-67 2600 Glostrup Tlf.: 24430136 E-mail: kasper.jessen(a)regionh.dk<mailto:kasper.jessen@regionh.dk> ________________________________ Denne e-mail indeholder fortrolig information. Hvis du ikke er den rette modtager af denne e-mail eller hvis du modtager den ved en fejltagelse, beder vi dig venligst informere afsender om fejlen ved at bruge svarfunktionen. Samtidig bedes du slette e-mailen med det samme uden at videresende eller kopiere den.

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V1 functional ROI
by Sarah Cole 15 Feb '18

15 Feb '18

Dear Dr. Douge, I am a little bit confused about creating function ROI in V1. Basically, I have some localizers that for some ROIs I need to find activated neurons in a specific contrast in native space and then create that ROI and map it to my experimental scans and extract their voxel data. I have used this command for right-FFA: funcroi-config -seg aparc+aseg.mgz 2007 -analysis eba-fba.native.rh -c faces-vs-objects -thresh 3 -sign pos -roi rh.surface.pSTS.faces-vs-objects.thr3.pos.roicfg -force But now, for V1 I am not sure what should I use. Is this correct? funcroi-config -seg aparc+aseg.mgz 400 -analysis eba-fba.native.rh -c faces-vs-objects -thresh 3 -sign pos -roi rh.surface.V1.faces-vs-objects.thr3.pos.roicfg -force I don't see a number in the lookup table for left and right V1. On the other hand, there are V1 labels in the label folder. I appreciate your help. Thanks

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Volume to Surface mapping looks great for Vols created in FSL but not SPM
by Rita Elena Loiotile 15 Feb '18

15 Feb '18

Hi, I'm trying to compare analyses that I've done entirely on the surface to analyses I've done in the volume. I'm comparing the analyses by projecting the volume analyses to the surface (HCP's 32k_fs_LR). The commands I'm using are: mri_vol2surf --mov $niftiFile --mni152reg --hemi ${hemi} --projfrac-max 0 1 0.2 --o ${giftiFile}.$hemi.gii; mri_surf2surf --srcsubject fsaverage --srcsurfval ${giftiFile}.$hemi.gii --trgsubject 32k_fs_LR --trgsurfval ${giftiFile}.$hemi.gii --hemi ${hemi}; It seems that the FSL volumes look identical to the surface analysis, when mapped. (Our surface analysis is mainly FSL-based, so this makes sense.) The SPM mapping, however, looks very odd. It isn't just that the intensity differs, but the localization of high intensity areas also varies. It seems that everything is shifted a bit superior and, possibly, posterior to the true location (as seen on the surface analysis). I'm wondering if I'm doing anything obviously wrong in my command usage. The brains were normalized to the MNI ICBM 152 template in SPM. I *think* it's suitable to use the -mni152reg flag in the command. I can attach pictures of the comparison if you'd like. Thanks in advance, Rita

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Removing labels after extending parcellation into white matter
by Michiko H. 15 Feb '18

15 Feb '18

Hi Freesurfer experts, I am wondering if it is possible to remove the original labels after extending the parcellation by 2mm into the WM for tractography? I don't wish to have tractography run on both sets of labels considering the algorithm would take into account the streamlines terminating at nodes defined by the labels so it doesn't quite make sense to count streamlines terminating at both the original label separately from the new label extending into the WM. I used the following command for growing the parcellation into WM: mri_aparc2aseg --s subj --annot aparc --wmparc-dmax 2 --labelwm --hypo-as-wm --o $SUBJECTS_DIR/$subj/mri/aparc+aseg+2mm.nii.gz Would appreciate help and suggestions! Thanks, Michiko.

3 5

QDEC Set Up
by Martin Juneja 15 Feb '18

15 Feb '18

Hi FS experts, I have two population groups X1 (controls) and X2 (patients). I am interested in calculating impact of sex (F or M) on causing difference between both groups e.g. I am interested in following 4 contrasts: X1 (F) > X1 (M) X2 (F) > X2 (M) X1 (F) > X2 (F) X1 (M) > X2 (M) X1 (M+F) > X2 (M+F) Could you please provide any directions on how can I set this up in QDEC (if possible) and/or by command line? Thanks.

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FIR analysis
by Sarah Cole 15 Feb '18

15 Feb '18

Hi experts, I was wondering if there is any tutorial or example on FIR analysis. I don't know where to start. I need to look at the time course of some voxels. I have a localizer session and the main experiment. I am intending to find the ROIs in the localizer scans and then extract their time course activation in the main experiment scans. I have done the recon-all successfully. Then in my localizer scan, I did preproc-sess, mkanalysis-sess with FIR 6 24 flag, mkcontarst, and selxabg3. Now, I am lost. Sorry for my naiive question. Thank you, --SC

2 1

inter-hemisphere registration on customised template
by Ting Qi 15 Feb '18

15 Feb '18

Dear Freesurfer experts, I am writing to ask how to do the surface-based inter-hemispheric registration based on the customised template, instead of fsaverage. I am planning to calculate the lateralisation index for each vertex, which means I should to use the symmetry template, for example, fsaverage_sym. However, the current issue is my participants are children. Therefore it would be better to put the individual data to the customised average template, which is already created by ANTS in my case. So I was wondering how to perform the symmetry registration on this created template? Thank you in advance. Cheers, Ting

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