Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30081 discussions

Hippocampus ROI
by Hua, Jessica 27 May '21

27 May '21

External Email - Use Caution Dear FreeSurfer experts, I am trying to create a hippocampus ROI in FSL (MNI 152_2mm brain space) from the FreeSurfer 7.0 hippocampal/amygdala segmentation. How do I create this ROI? Best, Jessica

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fspalm output
by Marina Fernández 27 May '21

27 May '21

External Email - Use Caution Dear experts, I used the function fspalm to run permutations with the following options: fspalm --glmdir /my_glmdir/ --cft 1.3 --name palm --iters 10000 --cwp .05 --onetail Checking the palmcofig.txt file that is generated as output, I realized that even if the "–logp" flag wasn't specified in the function, this flag is always applied with fspalm, and therefore the p-values of the *dpv_tstat_uncp.mgz file are saved as -log10(p). Consequently, if I want to threshold with p, I must first convert these values to p-values using 10^(- p) and then use p<0.05. In contrast, when I load the files *dpv _tstat_fwep.mgz and *clustere_tstat_fwep.mgz, the results don't appear to be -log10(p), and then these files wouldn't need to be transformed with 10^(- p) to use a threshold of p<0.05. What is the use of this flag in fspalm and why does it only affect the uncorrected p values? Thank you in advance. Marina

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Combined right and left analysis
by AJ 27 May '21

27 May '21

External Email - Use Caution Hi, I am trying to do long_stats_slopes on the aseg.stats file. Is there any way I could examine percent change as total thalamic or total corpus callosum instead of separately as right and left structures or various parts of CC? Thanks, AJ

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How to Specify External Regressor Files for FSFAST
by Eli Bulger 27 May '21

27 May '21

External Email - Use Caution Hello, I am working with task-based functional data pre-processed with fMRIPrep that I am trying to run through the FSFAST pipeline. I would like to use some of the nuisance regressors / confounds outputted by fMRIPrep as external regressors. The documentation for "mkanalysis-sess" (shown below) lists this as an option, but I am not sure how to go about creating the .bfloat file(s). Is there any documentation / example / tool that can provide some guidance on how to do this? Any advice is much appreciated! "mk-analysis-sess" documentation referred to: -extreg [extregstem] external regressor Use external regressors when doing estimation. The external regressors should be stored in the bfloat "volume" with stem extregstem. There should actually be only one file there (extregstem_000.bfloat). It should have one row, and the number of columns should be equal to the number of external regressors. The number of frames must be equal to the number time points. There should be an external regressor file in each run directory. By default, all the regressors will be used, but this can be changed with -nextreg. See also -mcextreg.

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Expression Syntax Error
by A.R. Sekar 27 May '21

27 May '21

External Email - Use Caution Hello experts, I am doing cerebellar segmentation from one of my previous posts using the command: isolate_labels.csh --vol aparc+aseg.mgz --outprefix aparc+aseg_labels --L $label 7,8,46,47 Following the command I am getting an expression syntax error: Akilas-MacBook-Air:B301001 akilasekar$ isolate_labels.csh --vol aparc+aseg.mgz --outprefix aparc+aseg_labels --L $label 7,8,46,47 Input file: aparc+aseg.mgz Output prefix: aparc+aseg_labels mri_convert aparc+aseg.mgz aparc+aseg.nii.gz reading from aparc+aseg.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) writing to aparc+aseg.nii.gz... Label of interest: 7,8,46,47 @: Expression Syntax. It would be great if you can help me solve this. Thanks! Akila

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help Optseq2 study design
by Ellen JOOS 27 May '21

27 May '21

External Email - Use Caution Dear Freesurfer team, I am currently preparing my first fMRI study and used OptSeq2 for creating the trial sequence. Since I am not experienced with the study design in MRI (I mainly conducted EEG studies so far), I would like to have your professional opinion on my design choices and use of your program. The parameters of my study are the following: I will conduct a multiband fMRI study with an event-related design that will have a TR of 0.5s. I will present 10 different types of trials that will have a length of 2.5s each, but that will be shown with different amounts of repetitions across the experiment. Within the 2.5s trial time, I included a fixed time period of 1.3s to respond. As indicated in your recommendations, I added time to the overall presentation time for the "NULL events" that corresponds to the time needed for one of my trial types (as if I would have another trial type). You can find the output of OptSeq attached. My questions are the following: 1) Did I use the program correctly by having a fixed response time window within the trial duration estimation? 2) Is the use of the NULL events (as can be seen in the attached file) correct and sufficient to introduce varying amounts of time between the individual trials such that the hemodynamic response can be captured appropriately? 3) In the summary of the OptSeq results, I found an efficiency value of 0.009 and a VRFAvg of 6.24. I saw in your recommendations that the VRFAvg should be 20-40. Is the result of my calcuation too bad to have an efficient recording that allows analyzing the data in an event-related manner? 4) In the actual experiment I will present the attached sequence twice. I have now the options to either present two different sequences (e.g. the two most efficient sequences produced by OptSeq) or to repeat the most efficient sequence twice. Do you have a recommendation? And further, might using the same sequence across participants result in a general ordering effect that might bias my results? I am very much looking forward to your response and already thank you for your advice and help! Kind regards, Ellen Joos -- Dr. rer. nat. Ellen JOOS INSERM U1114 Hôpital Civil / Clinique psychiatrique 1 place de l'hôpital 67085 STRASBOURG Tel: +33.3.88.11.61.31

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Re: [Freesurfer] Overlay of MGH clusters on Broadmann atlas
by Glasser, Matthew 27 May '21

27 May '21

External Email - Use Caution One reason Bruce may be asking why you need MNI coordinates is that MNI coordinates are a very poor substitute for surface-based statistical maps and a terrible way to compare across subjects. It’s much better to align subjects on the surface and then make much more accurate comparisons. If you have volume coordinates from an individual subject, you can project those accurately onto that subject’s cortical surface. In Connectome Workbench we do this with Foci, but I bet FreeSurfer has something similar. You just need to ensure that the coordinates and the surface are in the same volume space (i.e. are aligned with eachother). This could be in the subject’s physical space or MNI space (keep in mind that FreeSurfer never puts surfaces in MNI space, but we make copies of them there in the HCP Pipelines). I also see you asked how to convert .mgh to a Connectome Workbench readable format. I must admit I’m not entirely sure what .mgh contains. If it is a value per vertex, you could likely use mris_convert to do the conversion to .func.gii. .annot can be converted to .label.gii with mris_convert. Matt. From: <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of "Fischl, Bruce" <BFISCHL(a)mgh.harvard.edu> Reply-To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Date: Sunday, May 16, 2021 at 7:34 PM To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Overlay of MGH clusters on Broadmann atlas Hi Sara Why do you need MNI coordinates at all? Bruce From: freesurfer-bounces(a)nmr.mgh.harvard.edu <freesurfer-bounces(a)nmr.mgh.harvard.edu> On Behalf Of Romanella,Sara (BIDMC - Wilkinson - Neurology SF) Sent: Sunday, May 16, 2021 5:57 PM To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Overlay of MGH clusters on Broadmann atlas Hi Bruce, I can convert the MNI coordinates to subject space. But how do I enter them in freeview when I open the DK atlas of the subject to see where they fall? thank you for the help! Sara Romanella Fellow (Ph.D. in Neuroscience) Berenson-Allen Center for Noninvasive Brain Stimulation Department of Neurology | Beth Israel Deaconess Medical Center 330 Brookline Avenue, 02215 Boston, MA, USA Phone Nr: +1-339-229-7645 ________________________________ From: freesurfer-bounces(a)nmr.mgh.harvard.edu<mailto:freesurfer-bounces@nmr.mgh.harvard.edu> <freesurfer-bounces(a)nmr.mgh.harvard.edu<mailto:freesurfer-bounces@nmr.mgh.harvard.edu>> on behalf of Fischl, Bruce <BFISCHL(a)mgh.harvard.edu<mailto:BFISCHL@mgh.harvard.edu>> Sent: Sunday, May 16, 2021 10:31 AM To: Freesurfer support list Subject: [External] Re: [Freesurfer] Overlay of MGH clusters on Broadmann atlas Hi Sara Why do you need MNI at all? Why not just do it in individual subject space? Bruce From: freesurfer-bounces(a)nmr.mgh.harvard.edu<mailto:freesurfer-bounces@nmr.mgh.harvard.edu> <freesurfer-bounces(a)nmr.mgh.harvard.edu<mailto:freesurfer-bounces@nmr.mgh.harvard.edu>> On Behalf Of Romanella,Sara (BIDMC - Wilkinson - Neurology SF) Sent: Saturday, May 15, 2021 8:43 PM To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> Subject: Re: [Freesurfer] Overlay of MGH clusters on Broadmann atlas I am actually not sure. I have some MNI coordinates for the GM surface and I should check if they fall into a specific area of the DK. I could sacrifice accuracy in order to check this. Could you please me tell me how if possible? Thank you! Sara Romanella Fellow (Ph.D. in Neuroscience) Berenson-Allen Center for Noninvasive Brain Stimulation Department of Neurology | Beth Israel Deaconess Medical Center 330 Brookline Avenue, 02215 Boston, MA, USA Phone Nr: +1-339-229-7645 ________________________________ From: freesurfer-bounces(a)nmr.mgh.harvard.edu<mailto:freesurfer-bounces@nmr.mgh.harvard.edu> <freesurfer-bounces(a)nmr.mgh.harvard.edu<mailto:freesurfer-bounces@nmr.mgh.harvard.edu>> on behalf of Fischl, Bruce <BFISCHL(a)mgh.harvard.edu<mailto:BFISCHL@mgh.harvard.edu>> Sent: Saturday, May 15, 2021 6:04 PM To: Freesurfer support list Subject: [External] Re: [Freesurfer] Overlay of MGH clusters on Broadmann atlas Do you need to do that in a common space? The DK is a surface atlas and won’t map very accurately to MNI. I think Doug has something for this, but you will definitely sacrifice accuracy Bruce From: freesurfer-bounces(a)nmr.mgh.harvard.edu<mailto:freesurfer-bounces@nmr.mgh.harvard.edu> <freesurfer-bounces(a)nmr.mgh.harvard.edu<mailto:freesurfer-bounces@nmr.mgh.harvard.edu>> On Behalf Of Romanella,Sara (BIDMC - Wilkinson - Neurology SF) Sent: Saturday, May 15, 2021 5:56 PM To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> Subject: Re: [Freesurfer] Overlay of MGH clusters on Broadmann atlas Thank you in any case! Do you maybe know if I can enter MNI coordinates in freeview and see where it falls into the areas of DK atlas? Thank you! Sara Sara Romanella Fellow (Ph.D. in Neuroscience) Berenson-Allen Center for Noninvasive Brain Stimulation Department of Neurology | Beth Israel Deaconess Medical Center 330 Brookline Avenue, 02215 Boston, MA, USA Phone Nr: +1-339-229-7645 ________________________________ From: freesurfer-bounces(a)nmr.mgh.harvard.edu<mailto:freesurfer-bounces@nmr.mgh.harvard.edu> <freesurfer-bounces(a)nmr.mgh.harvard.edu<mailto:freesurfer-bounces@nmr.mgh.harvard.edu>> on behalf of Fischl, Bruce <BFISCHL(a)mgh.harvard.edu<mailto:BFISCHL@mgh.harvard.edu>> Sent: Saturday, May 15, 2021 5:47 PM To: Freesurfer support list Subject: [External] Re: [Freesurfer] Overlay of MGH clusters on Broadmann atlas Sorry, I don’t know what SimNIBS is (or how you can easily save a sphere in nifti format). Maybe someone else can comment? From: freesurfer-bounces(a)nmr.mgh.harvard.edu<mailto:freesurfer-bounces@nmr.mgh.harvard.edu> <freesurfer-bounces(a)nmr.mgh.harvard.edu<mailto:freesurfer-bounces@nmr.mgh.harvard.edu>> On Behalf Of Romanella,Sara (BIDMC - Wilkinson - Neurology SF) Sent: Saturday, May 15, 2021 5:41 PM To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> Subject: Re: [Freesurfer] Overlay of MGH clusters on Broadmann atlas Oh got it! It makes sense why I could not find it then! Thank you! Sorry for bothering again, but I have a similar issue on the DK atlas and I was wondering if you could also help me. I have some spheres saved in nifti in both MNI and/or subject's space (from SimNIBS), and I would like to see if they fall into a specific area of the DK atlas in FS. Do you have any suggestion how can I check this? Should I open the aparc+aseg DK atlas of the subject in freeview and somehow convert the nifti sphere and overlap them? The subject's space from SimNIBS and from FS output would be different? Thank you so much! Sara Sara Romanella Fellow (Ph.D. in Neuroscience) Berenson-Allen Center for Noninvasive Brain Stimulation Department of Neurology | Beth Israel Deaconess Medical Center 330 Brookline Avenue, 02215 Boston, MA, USA Phone Nr: +1-339-229-7645 ________________________________ From: freesurfer-bounces(a)nmr.mgh.harvard.edu<mailto:freesurfer-bounces@nmr.mgh.harvard.edu> <freesurfer-bounces(a)nmr.mgh.harvard.edu<mailto:freesurfer-bounces@nmr.mgh.harvard.edu>> on behalf of Fischl, Bruce <BFISCHL(a)mgh.harvard.edu<mailto:BFISCHL@mgh.harvard.edu>> Sent: Saturday, May 15, 2021 5:09 PM To: freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu> Subject: [External] Re: [Freesurfer] Overlay of MGH clusters on Broadmann atlas There should be the same BA labels on every subject, And no, not all of them, that is an ongoing project for neuroscience! Bruce From: freesurfer-bounces(a)nmr.mgh.harvard.edu<mailto:freesurfer-bounces@nmr.mgh.harvard.edu> <freesurfer-bounces(a)nmr.mgh.harvard.edu<mailto:freesurfer-bounces@nmr.mgh.harvard.edu>> On Behalf Of Romanella,Sara (BIDMC - Wilkinson - Neurology SF) Sent: Saturday, May 15, 2021 4:56 PM To: freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Overlay of MGH clusters on Broadmann atlas Hi Bruce, I did see there are some BA labels for each subjects, but not all of them is that right? Thank you! Sara Romanella Fellow (Ph.D. in Neuroscience) Berenson-Allen Center for Noninvasive Brain Stimulation Department of Neurology | Beth Israel Deaconess Medical Center 330 Brookline Avenue, 02215 Boston, MA, USA Phone Nr: +1-339-229-7645 ________________________________ From: freesurfer-bounces(a)nmr.mgh.harvard.edu<mailto:freesurfer-bounces@nmr.mgh.harvard.edu> <freesurfer-bounces(a)nmr.mgh.harvard.edu<mailto:freesurfer-bounces@nmr.mgh.harvard.edu>> on behalf of Fischl, Bruce <BFISCHL(a)mgh.harvard.edu<mailto:BFISCHL@mgh.harvard.edu>> Sent: Saturday, May 15, 2021 2:58 PM To: freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu> Subject: [External] Re: [Freesurfer] Overlay of MGH clusters on Broadmann atlas Hi Sara We keep statistics on each of the BAs separately, as stored in the various label files. During recon-all we put them together into a single non-overlapping .annot file that you can use for visualization on individual subjects. I thought he had done that for fsaverage also, but I looked briefly and didn’t see it, so you can just do it yourself if it would be useful. We’ll probably included it in future releases Cheers Bruce From: freesurfer-bounces(a)nmr.mgh.harvard.edu<mailto:freesurfer-bounces@nmr.mgh.harvard.edu> <freesurfer-bounces(a)nmr.mgh.harvard.edu<mailto:freesurfer-bounces@nmr.mgh.harvard.edu>> On Behalf Of Romanella,Sara (BIDMC - Wilkinson - Neurology SF) Sent: Saturday, May 15, 2021 12:23 PM To: freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Overlay of MGH clusters on Broadmann atlas Hi Bruce, thanks for the help, but I do not understand. Is there no template of BA atlas in fsaverage? Do I have to create it manually with the mris_label2annot? And in this case how should I do it? Thank you so much Sara Sara Romanella Fellow (Ph.D. in Neuroscience) Berenson-Allen Center for Noninvasive Brain Stimulation Department of Neurology | Beth Israel Deaconess Medical Center 330 Brookline Avenue, 02215 Boston, MA, USA Phone Nr: +1-339-229-7645 ________________________________ From: freesurfer-bounces(a)nmr.mgh.harvard.edu<mailto:freesurfer-bounces@nmr.mgh.harvard.edu> <freesurfer-bounces(a)nmr.mgh.harvard.edu<mailto:freesurfer-bounces@nmr.mgh.harvard.edu>> on behalf of Fischl, Bruce <BFISCHL(a)mgh.harvard.edu<mailto:BFISCHL@mgh.harvard.edu>> Sent: Saturday, May 15, 2021 11:45 AM To: freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu> Subject: [External] Re: [Freesurfer] Overlay of MGH clusters on Broadmann atlas Hi Sara You can assemble all the BA labels on fsaverage into a .annot file and display it that way if you want. mris_label2annot should do the trick. Just give it all the appropriate either with/without thresh (?h.BA*_exvivo.label or ?h.BA*_exvivo.thresh.label) Or just load the individual labels, which would be easy enough to do in a script to build the freeview command line Cheers Bruce From: freesurfer-bounces(a)nmr.mgh.harvard.edu<mailto:freesurfer-bounces@nmr.mgh.harvard.edu> <freesurfer-bounces(a)nmr.mgh.harvard.edu<mailto:freesurfer-bounces@nmr.mgh.harvard.edu>> On Behalf Of Romanella,Sara (BIDMC - Wilkinson - Neurology SF) Sent: Saturday, May 15, 2021 8:59 AM To: freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu> Subject: [Freesurfer] Overlay of MGH clusters on Broadmann atlas Hi FreeSurfer community, I have a cluster.mgh file (along with the .annot and .summary) resulting from correlation analysis of cortical thickness in a group of patients. I can open it as overlay in freeview but I was wondering if there was any chance to overlay it to a Broadmann atlas (hopefully in freeview) so I can visually show the overlap of the clusters with the BA areas. I cannot seem to find a Broadmann atlas in fsaverage to open in freeview. Also I was wondering, if I want to convert .mgh and open it on Connectome Workbench what extension do you think I should use (e.g., .gii). Should I use mri_convert or mris_convert? I am not sure if .mgh should be converted as a surface. Thank you so much for your help! Sara Sara Romanella Fellow (Ph.D. in Neuroscience) Berenson-Allen Center for Noninvasive Brain Stimulation Department of Neurology | Beth Israel Deaconess Medical Center 330 Brookline Avenue, 02215 Boston, MA, USA Phone Nr: +1-339-229-7645 ________________________________ This message is intended for the use of the person(s) to whom it may be addressed. 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Trouble with creating surface of macaque brain
by Singh, Shridhar (NIH/NEI) [C] 27 May '21

27 May '21

External Email - Use Caution Hi, I am trying to create a surface of a macaque brain, but I am running into issues with white matter. I segmented the white matter and manually edit wm.mgz, however the surf/?h.white output of recon all is not outlining everything in wm.mgz, creating problems with the surface. I attached an image demonstrating the problem. The red is wm.mgz and the yellow outline is lh.white. Why would regions identified as white matter in the left hemisphere of wm.mgz not be recognized as white matter in surf/lh.white, and what could I do to fix this issue? Also, when I run recon-all with the -autorecon2-wm flag, it seems that all my edits are reversed in wm.mgz. wm.seg.mgz is created by mri_segment, and then during mri_pretess, wm.mgz reverts back to what it was before my manual edits. Is there something wrong? Here's how I call recon-all: recon-all -autorecon2-wm \ -subjid ${subj} \ -cc-crs ${CC_string} \ -pons-crs ${PONS_string} \ -noaseg \ -xopts-use Thanks, Shridhar Singh

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Cerebellum Masks
by Erik O'Hanlon 27 May '21

27 May '21

External Email - Use Caution Dear Experts, Is it possible to use the SUITS labels (#601-628) in the LUT to make masks and extract volume measures. I ultimately want to use the masks for tractography purposes. Can I use the mri_extract to pull out the specific ROI's and if so do I use it with aparc+aseg file. Any details and guidance would be very much appreciated. Thanks Erik

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recon-all fails in Freesurfer7.1 on docker
by Lara Foland-Ross 26 May '21

26 May '21

External Email - Use Caution Hello, I'm trying to run Freesurfer7.1 on docker. I have a macbook air with an apple chip with BigSur as the OSX. To test out the installation, I ran recon-all on bert: recon-all -all -s bert The command quits with this error: "ERROR: cannot determine file type for /usr/local/freesurfer/subjects/bert/mri/rawavg.mgz Linux 8c70180fb77b 5.10.25-linuxkit #1 SMP PREEMPT Tue Mar 23 09:24:45 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux recon-all -s bert exited with ERRORS at Mon May 10 16:50:51 UTC 2021" I'm attaching the recon-all.log file. Could you please advise on how to troubleshoot? Many thanks, Lara Lara Foland-Ross, Ph.D. Senior Research Associate and Imaging Lab Manager Center for Interdisciplinary Brain Sciences Research Stanford University School of Medicine 401 Quarry Road, Room 1356 Stanford, CA 94305-5795

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