[Freesurfer] Average intensity from functional image within a label along the surface

External Email - Use Caution I am interested in obtaining the average intensity within a label from each frame of a functional image that has been smoothed on the surface (I have generated the label). However, the functional connectivity pipeline seems to use only volume

Re: [Freesurfer] question about longitudinal data analyses

On 7/9/2021 11:44 AM, Ritobrato Datta wrote: External Email - Use Caution Hi All, I have the following data – I have 205 subjects - each subject was imaged at 3 timepoints (baseline, followup 1 and followup 2) The 205 subjects are split in two treatment arms with 100 subjects

Re: [Freesurfer] LGI FS 7.1

External Email - Use Caution Would you normalize for differences in head size by adjusting for eTiV or total surface area? Thank you so much, Elisabetta Sent from my iPhone On Jul 9, 2021, at 2:08 PM, Douglas N. Greve wrote: I'm not sure what you mean. Can you elaborate? On

Re: [Freesurfer] Freesurfer longitudinal stream error

Try running it without the -parallel flag. If you want to use multiple cores, then add -threads N (N= number of cores) On 7/6/2021 4:29 AM, Susanne Gellißen wrote:     External Email - Use Caution Dear FreeSurfer Developers, I am processing MRI data using the freesurfer processing stream

Re: [Freesurfer] Visualizing specific cortical parcels in Desikan Killiany atlas

In FreeView, go to "View/Edit". From the resulting interface, you can turn on and off any parcellations you want. On 7/5/2021 1:04 PM, Ellen Ji wrote: > External Email - Use Caution > > Dear experts, > > I have a basic visualization question. > I would like to create a surface brain

Re: [Freesurfer] Transformation Applied to T1.mgz during recon-all

We refer to this operation as "conforming". This page might help https://surfer.nmr.mgh.harvard.edu/fswiki/FsAnat-to-NativeAnat On 7/4/2021 4:39 PM, Alexander Rockhill wrote: > External Email - Use Caution > > Hello, > >    I am trying to replicate the processing steps that occur

Re: [Freesurfer] setwdelay error 1 weight

By my count, you entered 36 weights. I'm not sure why it says you only entered 1, but try the correct number of weights first and see if the problem goes away On 7/3/2021 2:08 PM, Marilena Wilding wrote: External Email - Use Caution External Email - Use Caution Dear

Re: [Freesurfer] What is the relationship between qdec results and aparc.stats?

ROI-wise and vertex-wise analyses are different and may give different results. The vertex-wise analysis looks at individual vertices whereas ROI-wise averages over all the vertices. It is possible (even expected) that averaging over all vertices will reduce the variation and give stronger

Re: [Freesurfer] Hippocampal Subfield Definition Errors

Dear Franchesca, Could you please attach some images illustrating the problem? Cheers, /Eugenio Juan Eugenio Iglesias Senior research fellow CMIC (UCL), MGH (HMS) and CSAIL (MIT) http://www.jeiglesias.com On Jul 9, 2021, at 13:06, Franchesca Kuhney mailto:fkuh...@uic.edu>> wrote:

Re: [Freesurfer] Edit pial surface

You can use the reposition surface tool in freeview. Just be careful that you don't overwrite it if you re-run On 7/2/2021 3:37 AM, Rosalia Dacosta Aguayo wrote: External Email - Use Caution Dear Freesurfer's experts, I wonder if there is any chance to correct the pial surface when

Re: [Freesurfer] Question about Extracting QDEC Results

which results? sig maps (and other maps) are surface overlays. You can convert them to nifit format, but they will still be surface overlays (so you would not view/analyze them in FSL or SPM) On 7/1/2021 9:12 PM, Sonya Gupta wrote: External Email - Use Caution Hi, Hope you are

Re: [Freesurfer] Help segmenting all subjects in a folder

That does not apply to the recon-all command, only to mri_segment_hypothalamus_subunits On 7/1/2021 12:23 PM, g.ton...@libero.it wrote: External Email - Use Caution Hello FreeSurfer Developers, Thank you for your work ! I successfully set up Freesurfer and ran a test on my

Re: [Freesurfer] fcseed-config

you should not pass it a label. If you look at the help, Functional ROI-based options   -roi fcconfig : as created by funcroi-confg On 7/1/2021 10:58 AM, Nasiriavanaki, Zahra wrote: Hello Freesurferers, I’m trying to use a functional label (extracted from task functional BOLD data), as a

Re: [Freesurfer] Can I extract GLM values?

There should be a file called something like gamma.table.dat This is a text file with the differences for each ROI and contrast. On 7/1/2021 4:39 AM, Thalhammer, Melissa wrote: External Email - Use Caution Dear FS experts, I have run mris_preproc and mri_glmfit for group analysis as

Re: [Freesurfer] LGI FS 7.1

I'm not sure what you mean. Can you elaborate? On 6/30/2021 5:05 PM, Del Re, Elisabetta wrote: External Email - Use Caution External Email - Use Caution Thank you so much. I am still in doubt as to whether adjust/normalize for brain volume or otherwise surface area before

Re: [Freesurfer] mri_glmfit DOSS

You cannot use a DODS in this design as it tries to fit an offset and a slope for each class, which can't be done when the class has only one member. Try using DOSS instead. You should probably demean and rescale the eTIV to be between 0 and 1. On 6/29/2021 11:19 AM, Dr. Cornelius Kronlage

Re: [Freesurfer] recon-all soft errors

On 6/29/2021 3:32 AM, Rosalia Dacosta Aguayo wrote: External Email - Use Caution Dear Freesurfer team, I am inspecting the different participants I have run recon-all -all and I have found different errors I would like to discuss with you before proceeding as I am new with this

Re: [Freesurfer] Problem with mri_glmfit-sim

I think this might be a bug. You might be able to get around it by adding --no-perm-resid as the last option. Why are you running your own simulation instead of using the precomputed tables? On 6/28/2021 1:38 AM, juergen.haen...@upd.unibe.ch wrote: External Email - Use Caution Dear

[Freesurfer] Hippocampal Subfield Definition Errors

External Email - Use Caution Hello, I've run into an issue with the longitudinal hippocampus/amygdala segmentation (segmentHA_T1_long.sh). All of the commands ran properly and I got the outputs listed on the FreeSurfer wiki but, upon QAing the segmentations, I realized that a few

Re: [Freesurfer] smoothing volume data extracted using aparcstats2table

Generally, you do not smooth it as averaging over the ROI is effectively a type of smoothing. If you were to smooth prior to the averaging, you'd get one area smearing into another. On 6/28/2021 12:57 PM, Ryan Bell, Ph.D. wrote: External Email - Use Caution Dear Freesurfer Experts,

Re: [Freesurfer] Calculating group-wise Dice Similarity Coefficient and corresponding surface map

try $FREESURFER_HOME//matlab/annotval2surfoverlay.m On 6/25/2021 2:55 PM, Fischl, Bruce wrote: I guess doing it in matlab would be easiest *From:* freesurfer-boun...@nmr.mgh.harvard.edu *On Behalf Of *Hye Min Shin *Sent:* Friday, June 25, 2021 1:24 PM *To:* freesurfer@nmr.mgh.harvard.edu

Re: [Freesurfer] Cortical thicknees normalization values

We generally do not normalize it by anything. ICV norm is not needed because thickness does not scale with head size. Sometimes people will normalize by mean thickness, but that changes the question being answered, so that is more a question for you On 6/24/2021 3:01 PM, Gabbo Ramírez García

[Freesurfer] question about longitudinal data analyses

External Email - Use Caution Hi All, I have the following data – I have 205 subjects - each subject was imaged at 3 timepoints (baseline, followup 1 and followup 2) The 205 subjects are split in two treatment arms with 100 subjects in the first one and 105 subjects in the

[Freesurfer] Tracula 7.1.1 - trac-all - stat

External Email - Use Caution Hello FreeSurfer Developers, I am just started to use "the trac-all -stat" command of Tracula 7.1.1 to reconstruct a mean tract for each pathway for all the subjects of a group. Several files are created for each pathway in the "stat" directory.