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19 participants
30088 discussions

converting correlation coefficient file into a table
by Wenzhen Zhao 27 Jun '19

27 Jun '19

External Email - Use Caution Dear List, I finished first level analysis of functional connectivity of all subjects with respect to Left hippocampus, and have several files (ces.nii.gz, pcc.nii.gz). Is there any command that I can convert this particle correlation coefficient (which I assume contain correlation coefficient of each voxel to Left hippocampus, please correct me if I am wrong) into a table showing functional correlation between left hippocampus and other ROIs ? Thanks, Wenzhen

2 1

recon-all multiple subjects 'for' loop?
by Benjamin Stott 27 Jun '19

27 Jun '19

External Email - Use Caution Hello, I would like to run recon-all on multiple subjects. I have 650 subjects, so running them in separate terminals isn't an option. Each subject has their own folder (e.g. sub-CC121428) containing a single T1w.nii.gz file. Unfortunately, I have very little experience coding. I appreciate any advice you can offer. Benjamin

2 3

mri_glmfit will not use mask or label
by Jennifer Legault 27 Jun '19

27 Jun '19

External Email - Use Caution Hi Freesurfer experts, I'm trying to constrain my sMRI analysis to only search for brain regions (GMV) that are correlated with a behavioral measure within a mask (made from a functional contrast of interest, so that I'm only searching for regions that were shown to be active during a language localizer task) using mri_glmfit. I've followed recommended steps to transforming my fMRI contrast into a surface mask, and then later even tried making it into a surface label, however whenever I run the analysis, I get the same results regardless of whether I use the --mask or --label option, meaning that the summary file (cache.th40.pos.sig.cluster.summary) includes regions that are outside the mask. How can I ensure that mri_glmfit actually uses the mask? I've included below the commands I have run. I previously ran mri_glmfit to search the whole brain for regions significantly correlated with behavioral measures using the following command: mri_glmfit --y fsgd_VSL_std_age_gender_TIV.volume.00B.mgh --fsgd fsgd_VSL_std_age_gender_TIV.txt --C Contrast_VSL_std_a_g_TIV.txt --surf fsaverage lh --cortex --glmdir lh.VSL_std_age_gender_TIV.glmdir Now, when I try to use the mask, I get the same results as above (significant result in regions outside of mask), using the following command: mri_glmfit --y fsgd_VSL_std_age_gender_TIV.volume.00B.mgh --mask localizer_mask.mgh --fsgd fsgd_VSL_std_age_gender_TIV.txt --C Contrast_VSL_std_a_g_TIV.txt --surf fsaverage lh --cortex --glmdir lh.VSL_std_age_gender_TIV_localizer_mask.glmdir I also converted the mask into a label just in case, and used the following command: mri_glmfit --y fsgd_VSL_std_age_gender_TIV.volume.00B.mgh --label <path>/freesurfer/fsaverage/label/LeftMidAntTemp_surf.label --fsgd fsgd_VSL_std_age_gender_TIV.txt --C Contrast_VSL_std_a_g_TIV.txt --surf fsaverage lh --cortex --glmdir lh.VSL_std_age_gender_TIV_localizer_label.glmdir Across all these conditions, I always get the same results (even if the significant region is outside of the mask). Are there any recommendations for steps I should take to make sure I'm only searching for regions inside the mask? Best, Jen -- Jennifer Legault PhD, Neuroscience Postdoctoral Scholar Language Acquisition and Brain Lab University of Delaware

2 2

BA label questions
by Zeng,Victor (BIDMC - Psychiatry) 27 Jun '19

27 Jun '19

?Hi All, I'm revisiting an old dataset that was previously run using FS 5.1, and now we upgraded it to FS 6.0. I seem to notice there are different set of BA.labels, ones that are called ?h.BA.label, and ones (generated from 6.0) called ?h.BA_exvivo.label. Is ?h.BA.label deprecated by ?h.BA_exvivo.label? If not, what are the differences and how can we make ?h.BA.label in FS6.0? Victor Zeng Beth Israel Deaconess Medical Center Keshavan Lab ph: 617 754 1237 -- ________________________________ This message is intended for the use of the person(s) to whom it may be addressed. It may contain information that is privileged, confidential, or otherwise protected from disclosure under applicable law. If you are not the intended recipient, any dissemination, distribution, copying, or use of this information is prohibited. If you have received this message in error, please permanently delete it and immediately notify the sender. Thank you.

2 1

Labelling SurfStat p-value surface map
by Loïc Daumail 27 Jun '19

27 Jun '19

External Email - Use Caution Dear Freesurfer community, I obtained score matrices of surfaces after performing diffusion embedding map on fMRI data. I am now using the SurfStat toolbox(Matlab) in order to obtain p-value maps to compare between two groups. After obtaining the p-value map, I would like to label the surface in order to identify the regions of significant difference between both groups. Would it be possible to use Freview in order to do it? If so, which format should I use for my SurfStatP output p-value map? How would you do it, (tools to convert into a specific format, surfaces and atlas to load on Freeview, which format for those ones)? I would be very grateful if you could detail a bit, as I am new to these tools! Thanks in advance, Loïc Daumail

4 27

Help for smoothing the pial surface
by Nillo, Ryan Michael R 27 Jun '19

27 Jun '19

Hello FreeSurfer users/developers, I want to generate a smooth pial surface similar to the one displayed on the LGI page (https://surfer.nmr.mgh.harvard.edu/fswiki/LGI <https://surfer.nmr.mgh.harvard.edu/fswiki/LGI>) without having to run the entire recon-all process. Additionally, I want to map this surface to the white surface. Is there an easy way to do this? Thanks in advance, Ryan Michael Nillo Staff Research Associate I University of California San Francisco Department of Radiology and Biomedical Imaging External Email - Use Caution

2 1

Viewing clusters regardless of significance
by Amrita Bedi 26 Jun '19

26 Jun '19

External Email - Use Caution Hi Freesurfer developers, I’m using the glmfit tutorial to see clusters for my data. I’m trying to view the uncorrected clusters on tksuefer using the command line tksurfer fsaverage lh inflated -overlay /path to data/cache.th13.abs.sig.ocn.annot but don’t see any clusters. According to the cluster summary file there should be 2 clusters on the left hemisphere and 9 on the right. Thank you for your help.

1 0

Applying transformation to surface (e.g. pial) files
by Puzniak, Robert 26 Jun '19

26 Jun '19

External Email - Use Caution Hello, first of all, please forgive me a trivial question, but digging through archives neither provided me with a simple answer, nor gave me an idea how to solve the problem in an elegant way. What I need to do is to apply transformation matrix (actually it's a "ras xform", I can extract it with mri_info and create .xfm file) to the surf/?h.pial files. I'll be very grateful if You could hint me how to approach this, as my attempts with mris_convert, tkregister2 and mri_surf2surf weren't successful. Kind regards, Robert -- M.Sc. Robert Puzniak Marie Curie Fellow - NextGenVis Network Visual Processing Lab, Ophthalmic Dpt. Otto-von-Guericke-Universitaet Leipziger Str. 44 39120 Magdeburg, Germany ++49 (0)391 67 21722

1 0

Interpretation question during LME steps
by Daliah Ross 26 Jun '19

26 Jun '19

External Email - Use Caution Hello FreeSurfer Developers, I am working on running a mass-univariate linear mixed effects model with cortical thickness data, and I have a question about the step that segments the initial covariance estimates into homogenous regions. The next step from the LME webpage (figure; p1 = patch(surf); …) creates figures of the left hemisphere projected onto a sphere and shows clusters of the significant vertices. I am having trouble interpreting this spherical figure. Can it be opened in freesurfer, (i.e. in freeview or tksurfer), so that I can see these clusters projected onto, for example, the inflated cortex (e.g. of fsaverage)? Thank you, Daliah Ross *Daliah Ross* | dross3(a)mail.yu.edu Ph.D. Student, Clinical Psychology with Health Emphasis Ferkauf Graduate School of Psychology Yeshiva University Albert Einstein College of Medicine

2 1

Problem for LGI
by Gwang-Won Kim 26 Jun '19

26 Jun '19

2 1

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