[Freesurfer] Surface based paired t test

External Email - Use Caution Dear Freesurfer experts, I would like to run surface based paired t test of PET data on surface. For every subject I have visit pre treatment and post treatment. I tried to follow the instructions here https://surfer.nmr.mgh.harvard.edu/fswiki/Paired

[Freesurfer] average of surfaces

External Email - Use Caution Dear Freesurfer experts, I have multiple PET volumetric images in MNI standard space. I can average (or get the Tmean) of these images using fslmerge then fslmaths. I would like to do something similar on surfaces images. I registered the images from

Re: [Freesurfer] Surface based paired t test

this command to fit PET data mris_preproc --target fsaverage --hemi lh \ --meas thickness --out lh.paired-diff.thickness.mgh \ --fsgd pairs.fsgd --paired-diff Thanks for any help! John ‐‐‐ Original Message ‐‐‐ On Tuesday, November 20, 2018 6:34 PM, john Anderson wrote: > Dear Fr

[Freesurfer] Surface based paired t test

how can I modify this command > to fit PET data > > mris_preproc --target fsaverage --hemi lh \ >--meas thickness --out lh.paired-diff.thickness.mgh \ >--fsgd pairs.fsgd --paired-diff > > Thanks for any help! > John > > ‐‐‐ Original Message ‐‐‐ > On

[Freesurfer] Fw: Surface based paired t test

eproc with --help to get examples On 12/06/2018 12:31 PM, john Anderson wrote: > > External Email - Use Caution > > Hi Dr Greve, >> I tried to follow this web page >> https://surfer.nmr.mgh.harvard.edu/fswiki/PairedAnalysis >> This tutorial seems to be

[Freesurfer] Surface based analysis - circular analysis?

External Email - Use Caution Dear experts, I have three groups: - pre treatment (baseline) - post treatment (follow-up after 6 month of the baseline visit) - healthy controls. The three groups have PET data. I ran surface based paired t test between pre and post treatment. The a

[Freesurfer] fsaverage, brainstem and cerebellum

External Email - Use Caution Dear FS experts, For visualization purposes, is there any way to show the cerebellum and brain stem regions (similar to the attached figure), this figure was published used CONN toolbox but I am not sure how they were able to map functional data in b

Re: [Freesurfer] fsaverage, brainstem and cerebellum

with mris_smooth and load them into freeview. Shouldn't be too hard. cheers Bruce On Thu, 10 Jan 2019, john Anderson wrote: ‐‐‐ Original Message ‐‐‐ On Thursday, January 10, 2019 7:40 AM, john Anderson wrote: > Dear FS experts, > For visualization purposes, is there any

Re: [Freesurfer] fsaverage, brainstem and cerebellum

.mgs with fsaverage I believe. You can just > tesselate that. > > cheers > Bruce > On Thu, 10 Jan 2019, john Anderson wrote: > > > External Email - Use Caution > > Hi Dr Bruce, I highly appreciate your guidance. > > I would like to load the cerebellum and brain

[Freesurfer] Average of surfaces

External Email - Use Caution Dear FS experts, I resampled PET images for multiple subjects I used mri_vol2surfe to move these images onto fsaverage, not I have for every subject lh.PET and rh.PET How can I create the average of multiple surfaces. For example: on the left hemisphe

[Freesurfer] mapping a volumetric statistical map to the cerebellum surface

External Email - Use Caution Dear FS experts, I have a statistical map from the output of a surface based analysis in subcortical regions. This statistical map shows significant difference between the groups in the cerebellum cortex. I reconstructed the cerebellar surfaces using

Re: [Freesurfer] fsaverage, brainstem and cerebellum

commands to improve the topology of these structures? Your guidance is appreciated, John Sent with ProtonMail Secure Email. ‐‐‐ Original Message ‐‐‐ On Thursday, January 10, 2019 1:37 PM, john Anderson wrote: > Ah! great!! thank you so much for the great help!! > Have a good day,

Re: [Freesurfer] fsaverage, brainstem and cerebellum

topologically correct. > > cheers > Bruce > > > On Tue, 22 Jan 2019, john Anderson wrote: ‐‐‐ Original Message ‐‐‐ On Tuesday, January 22, 2019 7:36 AM, john Anderson wrote: > Hi Dr Bruce, > I applied your recommendations and I was able to create surfaces to the &

Re: [Freesurfer] mapping a volumetric statistical map to the cerebellum surface

n specific structural surfaces such as cerebellum and brain stem? Thanks John Can you be more specific about how mri_vol2surf failed? Eg, command line, terminal output, reason you think it did not work On 1/21/19 10:47 AM, john Anderson wrote: > > External Email - Use Cautio

[Freesurfer] correction for multiple comparison: simulation vs grf vs cache

External Email - Use Caution Hi Dr Greve, I would like to correct surface based analyses of PET data for multiple comparisons. I ran group comparisons in three spaces. left and right hemispheres and subcortical. I used the method --cache in mri_glmfit-sim to correct the analyses

[Freesurfer] move statistical map onto the cerebellum surface

External Email - Use Caution Dear FS experts, I ran surface based PET analysis on subcortical regions. Then corrected the results for multiple comparisons using the method --grf in the command mri_glmfit-sim. I can visualize the output of multiple comparisons (i.e. the file gr

Re: [Freesurfer] move statistical map onto the cerebellum surface

n if it is the entire cerebellum as FS commands generally require a hemisphere. The run mri_vol2surf specifying --hemi lh --surf cerebellum On 1/23/19 10:04 AM, john Anderson wrote: > > External Email - Use Caution > > Dear FS experts, > I ran surface based PET analys

Re: [Freesurfer] move statistical map onto the cerebellum surface

send the full terminal output? On 1/24/19 4:56 PM, john Anderson wrote: > > External Email - Use Caution > > Hi Dr Greve, I appreciate your guidance very much. > > I followed your suggestion. I put lh.cerebellum in fsaverage and I ran > mri_vol2surf. > as follow

[Freesurfer] dtrecon

External Email - Use Caution Hi FS experts, I would like to inquire about the command "dtrecon" in Freesurfer. Is this command able to process multishell diffusion data? if not would you recommend any method? Thanks in advance John___ F

[Freesurfer] mri_convert

External Email - Use Caution hi FS experts. I would like to inquire about the command mri_ convert I use this command to convert fMRI and PET 4D volumes from dicom format to nifti. Are there any flags that can be used in mri_convert command line to enable it to extract a text fi

Re: [Freesurfer] mri_convert

much! John you mean you want the acquisition times to do kinetic modeling? I don't have anything to do that. Also, you should check to see whether your PET has intensity scaling imbedded in the dicom as the v6 mri_convert does not handle this properly. On 2/20/19 11:44 AM, john

[Freesurfer] petsurfer Kinetic Modeling (MRTM1, MRTM2)

External Email - Use Caution Hi Dr Greve, I would like to use petsurfet to do kinetic modeling (KM), the pipeline is straightforward and easy to use. Thank you so much! I would appreciate any clarifications relevant to my questions bellow: 1) I understand that the flag "--km-ref"

Re: [Freesurfer] petsurfer Kinetic Modeling (MRTM1, MRTM2)

.ctab. Is there any way to let --km-ref know that I want to do whole brain normalization without feeding a very long list of numbers? Thank you so much for help John On 2/22/19 7:58 AM, john Anderson wrote: External Email - Use Caution Hi Dr Greve, I would like to use petsurfet to d

Re: [Freesurfer] petsurfer Kinetic Modeling (MRTM1, MRTM2)

this flag represent regions of high binding affinity in patients or healthy controls or it doesn't matter just regions known to have high binding. For example some tracers show regions of high binding affinity on healthy scans as well as patients scans. On 2/22/19 11:43 AM, john

[Freesurfer] mni152reg

External Email - Use Caution Dear FS experts, I would like to move PET image to MNI152. What is the correct command to do so. I tried mri_vol2vol --mov PET.nii.gz --s subjID --targ $SUBJECTS_DIR/subjID/mri/orig.mga --regheader --o PET_T1.nii.gz mni152reg --s subjID then mri_vol2

[Freesurfer] mri_synthmorph

External Email - Use Caution Dear Freesurfer experts, I processed DTI data using dt_recon, and I want to register FA images to the standard MNI152 space. However, after running the command mri_synthmorph fa.nii.gz template.nii.gz -o fa_in_MNI.nii.gz, the registration is not accura

Re: [Freesurfer] mri_synthmorph

; Cheers, > Malte > > > From: freesurfer-boun...@nmr.mgh.harvard.edu < > freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of John Anderson < > jb19790...@gmail.com> > Sent: Friday, September 1, 2023 12:45 > To: Freesurfer sup

Re: [Freesurfer] mri_glmfit-sim - Clusterwise correction for multiple comparisons.

External Email - Use Caution assuming that all preprocessing steps, fsgd file and contrasts are correct, the choice between doss and dods could explain some of the variability you're seeing in your results. Consider running both models and possibly additional validation to see whic

Re: [Freesurfer] data quality check before analysis [EXTERNAL]

External Email - Use Caution - FreeSurfer 5.3 QA Tools https://secure-web.cisco.com/1xhhgMhrQlSBmGkb8NMn06KLlNRaz3DnQ7vzdZdQzrqjoeDsU5-gpo8VaUCxtX79W2O5j9rC87MnVFoBXzpHmSrCDzkZXGGR7I_PmSZlic0yw_BJBu2NDNAuQxkdpXtMPVHqiMbinZ5ak8HWwws2ZWPYgfTlbVjDSje40bRgu0R5XIZ3hox3WQjltQwACheB5Jq32

Re: [Freesurfer] data quality check before analysis [EXTERNAL]

3A*2F*2Fwww.yahoo.com__;JSUl!!NZvER7FxgEiBAiR_!q-NbuKT23td_9o4DVH6jwPBlnCTPblT-heTmAHOlh6z6ucR3zZIfrZ4zbIojHZWpC28OyCiJjDFgI-IJC6-Qp_YtDOe9CqExedn8dmq0OW4$>* +98 914 526 9298 On Saturday, October 14, 2023 at 03:29:11 PM GM

[Freesurfer] Distance Measurement After recon-all

External Email - Use Caution Dear FreeSurfer experts, I would like to know if there is a command in FreeSurfer that can help me measure the distance (in voxels or mm) between a lesion mask and the closest voxels in the ribbon after applying recon-all to T1 images. Thanks for your a

Re: [Freesurfer] Distance Measurement After recon-all

appreciate your suggestions. Thank you John On Mon, Nov 20, 2023 at 7:13 AM John Anderson wrote: > Dear FreeSurfer experts, I would like to know if there is a command in > FreeSurfer that can help me measure the distance (in voxels or mm) between > a lesion mask and the closest voxels in t

[Freesurfer] cortocal thickness / gray matter volume

External Email - Use Caution Dear experts, this is the first time I have used Freesurfer. I am a clinician and I don't have previous experience. I followed wiki instructions. I have a group of T1 images. I need cortical thickness and cortical gray matter volume measurements . I ran

[Freesurfer] change labels name

External Email - Use Caution Dear Freesurfer, I have a volumetric atlas in nifti format. I can open this atlas in freeview. Using the Lookup Table>FreesurferColorLUT, I can see how every label has a specific color. When I move the mouse cursor over an area of this atlas. I can see

Re: [Freesurfer] MRI image quality metrics

External Email - Use Caution You might consider the command wm-anat-snr to compute SNR On Thu, Feb 9, 2023 at 10:38 AM Kumar, Avnish wrote: > You could also use these: > >1. For CNR you can use the mri_cnr tool: > > mri_cnr [options] > > For example: > > mri_cnr $SUBJECTS_

Re: [Freesurfer] MRI image quality metrics

qrt(gray_var), sqrt(csf_var) > > label : read hemisphere labels from and > > -u, -?, -help : print usage information and quit > > -version : print software version information and quit. > > On Thu, Feb 9, 2023 at 3:46 PM John Anderson wrote: > >> Exte

[Freesurfer] mri_segstats

External Email - Use Caution Dear Freesurfer community, Please forgive me for the basic nature of my question. I was wondering whether there is an argument that can be included in mri_segstats to display the results in cubic centimeters (cm^3) instead of cubic millimeters (mm^3). t

[Freesurfer] mri_convert mosaic data

External Email - Use Caution Dear Freesurfer, I have ASL DICOM data from a Siemens scanner in mosaic format. For each subject, there are 64 DICOM files, which consist of both tags and controls. I would like to convert each individual DICOM into a separate NIfTI file or a single 4D

Re: [Freesurfer] mri_convert mosaic data

rt those DICOMs? It will use dcm2niix to > convert. > > > > Best, > > > > Yujing > > > > *From:* freesurfer-boun...@nmr.mgh.harvard.edu < > freesurfer-boun...@nmr.mgh.harvard.edu> *On Behalf Of *John Anderson > *Sent:* Wednesday, March 15, 2023

[Freesurfer] mri_convert mosaic dicoms

External Email - Use Caution Dear Dr Doug Greeve, For each participant in my dataset, I have 8 mosaic volumes with 36 slices each. I am trying to convert the DICOM files to Nifti format using the mri_convert command in FreeSurfer version 7.3.2. However, the conversion process fails

Re: [Freesurfer] mri_convert mosaic dicoms

e a NIfTI image with multiple volumes as expected by using the mri_convert command with the --nslices-override argument, but I'm not sure if I'm using it correctly. On Mon, Mar 27, 2023 at 11:19 AM Douglas N. Greve wrote: > Can you try it with --dcm2niix ? > > On

[Freesurfer] mri_glmfit correction across lobes

External Email - Use Caution Hello Freesurfer, Currently, I am using the Petsurfer manual, which is easily understandable and clear. Nonetheless, I have a question regarding the "mri_glmfit" step. As far as I know, this command is used to correct data for multiple comparisons among

Re: [Freesurfer] mri_glmfit correction across lobes

rect for multiple comparisons. For ROI-based > analyses, you can use bonferroni or FDR. For maps you can use > mri_glmfit-sim. > > On 4/4/2023 4:53 PM, John Anderson wrote: > > External Email - Use Caution > Hello Freesurfer, > Currently, I am using the Petsurf

[Freesurfer] questions about mri_normalize

External Email - Use Caution Dear experts, I have been using the mri_normalize in FSv7.3.2 to standardize the intensity of FLAIR images , and I've observed that increasing the sigma parameter up to 25 is effective in improving the quality of the normalized images for noisy datasets

[Freesurfer] Fwd: questions about mri_normalize

External Email - Use Caution Dear experts, I have been using the mri_normalize in FSv7.3.2 to standardize the intensity of FLAIR images , and I've observed that increasing the sigma parameter up to 25 is effective in improving the quality of the normalized images for noisy datasets

Re: [Freesurfer] Size of overlap between a label and a volume

External Email - Use Caution Let's say the red spot is overlay.nii.gz 1) convert aparc+aseg from mgz to nii.gz using: mri_convert aparc+aseg.mgz aparc+aseg.nii.gz 2) create mask between overlay and the atlas using fslmaths: fslmaths aparc+aseg.nii.gz -mas overlay.nii.gz overlay_ove

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