[Freesurfer] Registration of MPF to FLASH 3D image

External Email - Use Caution Dear Freesurfer team, I messaged the team on my MPF map analysis and a suggestion was made that I register the MPF maps on the T1 MPRAGE images. However, I did not acquire MPRAGE but FLASH images. Can I used those instead ? Again, I tried even using

[Freesurfer] Parallel Command for Windows

External Email - Use Caution Hi Freesurfer team, Please can I run the parallel Command for freesurfer? I am using windows 11. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/f

[Freesurfer] Freesurfer Intensity representation

External Email - Use Caution Hi, Please I made an initial enquiry about using freesurfer for MPF maps. The feedback was that I register the MPF maps on their corresponding T1 images using multimodal registration. I used FSL to do the multimodal registration and then use recon-all

Re: [Freesurfer] Freesurfer Intensity representation

olume you gave as input to recon-all. If you tell us which > statistics you want to regenerate for another volume we can tell you know > what commands to run. > > > cheers > > Bruce > > > > *From:* freesurfer-boun...@nmr.mgh.harvard.edu < > freesurfer-boun...@

Re: [Freesurfer] Freesurfer Intensity representation

mean that the intensity is from the MPF. On Wed, Jan 24, 2024 at 6:44 PM ERNEST KISSI wrote: > I want to use the intensity of the macromolecular proton fraction (MPF). I > want to compare the intensity of the MPF between two groups. > > On Wed, Jan 24, 2024 at 6:11 PM Fischl,

Re: [Freesurfer] Freesurfer Intensity representation

alter the signal intensity or contrast of the MPF images. Therefore, the registered MPF images still reflect the macromolecular proton fraction of the brain tissue, which is independent of the T1 values. Just wanna confirm. This is from a colleague. On Wed, Jan 24, 2024 at 6:50 PM ERNEST KISSI

[Freesurfer] Intensity Representation

External Email - Use Caution Dear Freesurfer Team, I registered a Macromolecular Proton Fraction (MPF) map on T1 image using multimodal registration in FSL and used freesurfer for the parcellation as instructed by one of your colleagues. I want to really confirm that whether the

[Freesurfer] Calculation of MRI intensity

, Ernest Kissi Kontor. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e

[Freesurfer] Tissue Segmentation

External Email - Use Caution Hello freesurfer team, Please does Freesurfer have a function or a code for tissue Segmentation just like in FSL that you can do tissue based segmentations into GM, WM and CSF and also their partial volume segmentations? Thank you. ___

[Freesurfer] Grey Matter Intensities

External Email - Use Caution Hi Freesurfer team, Recon-all output shows the white matter volumes and white matter intensities of different brain regions but only shows grey matter volumes. I want to know if there is a function or a flag to also get information on the regional gre

[Freesurfer] Using MRI_segstats to calculate grey matter intensity

External Email - Use Caution Hello freesurfer Team, I have the grey matter segmentation from FSL and I have freesurfer recon-all output but the recon-all outputs do not have regional grey matter intensities. Can I use MRI_segstats to calculate the regional grey matter output using

Re: [Freesurfer] Grey Matter Intensities

> Are these what you are looking for? They should work the same way as aseg > volume. > > > > Best, > > > > Yujing > > > > *From:* freesurfer-boun...@nmr.mgh.harvard.edu < > freesurfer-boun...@nmr.mgh.harvard.edu> *On Behalf Of *ERNEST KISSI > *Sen

Re: [Freesurfer] Grey Matter Intensities

gray matter > intensity within each cortical parcel and each subcortical structure. Is > that what you want? > > > > *From:* freesurfer-boun...@nmr.mgh.harvard.edu < > freesurfer-boun...@nmr.mgh.harvard.edu> *On Behalf Of *ERNEST KISSI > *Sent:* Wednesday, February 21, 202

Re: [Freesurfer] Grey Matter Intensities

t and see if it does what you want. I believe it is also run by default > during recon-all and the values placed into one of the stats output files > > > > Cheers > > Bruce > > > > *From:* freesurfer-boun...@nmr.mgh.harvard.edu < > freesurfer-boun...@nmr.m

Re: [Freesurfer] Grey Matter Intensities

.edu < > freesurfer-boun...@nmr.mgh.harvard.edu> *On Behalf Of *ERNEST KISSI > *Sent:* Wednesday, February 21, 2024 12:52 PM > *To:* Freesurfer support list > *Subject:* Re: [Freesurfer] Grey Matter Intensities > > > > *External Email - Use Caution* >

[Freesurfer] How to write rh.w-g.pct from recon-all stats output into a table

External Email - Use Caution I processed several items of data. And I have rh.w-g.pct file in my stats folders. How can I get process this file to get table reading file? I tried to use asegstats2table and aparcstats2table but it didn’t work. Could you provide me with necess

[Freesurfer] Intensity affected after using -c flag in mri_convert

External Email - Use Caution Dear fresurfer team, Why does the use of conform flag (-c) in mri_convert affect the intensity of the image? I have an image with absolute intensity of 1000 and after using the conform flag in mri_convert, the intensity is around 98.1. why is there a

[Freesurfer] Calculating intensity of Individual voxel

External Email - Use Caution Hi, freesurfer team Is there a way to calculate the intensity of a voxel.Let say, I have a voxel with coordinate 20, 30 and 34 and I wanna know the intensity of it. Can it be done in freesurfer? ___ Freesurfe

Re: [Freesurfer] Calculating intensity of Individual voxel

frames. > > > > Best, > > > > Yujing > > > > *From:* freesurfer-boun...@nmr.mgh.harvard.edu < > freesurfer-boun...@nmr.mgh.harvard.edu> *On Behalf Of *ERNEST KISSI > *Sent:* Friday, June 21, 2024 5:16 AM > *To:* Freesurfer support list > *Subj

[Freesurfer] Negative voxel ranges

External Email - Use Caution Dear fresurfer team, Please I want to extract the intensity of a voxel 48, -56, -34. But my voxel ranges of my image does not include negative values. Is there a way to make the ranges cover these values. Thanks 👍. ___