You have to give it a t1-weighted image.
On 1/7/2025 10:31 AM, Pandey, Shraddha wrote:
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Hi, Thank you for your response. The images in the first figure represent the paramagnetic files (output from the Chi Separation algorithm). The |lh.white| surface, registered using the |transformationvolume.dat| file, has been overlaid on the paramagnetic volume (2nd Figure). Thanks, Shraddha
*From:* freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N. Greve dgreve@mgh.harvard.edu *Sent:* Monday, January 6, 2025 9:12 AM *To:* freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] [External] Re: Assistance with mri_vol2surf: Missing Surface Values in Output
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What kind of image is that? FS will only work on T1-weighted. I'm surprised it did that good.
On 1/3/2025 2:12 PM, Pandey, Shraddha wrote:
* External Email - Use Caution * Hi, Thank you for your response. I suspect the gray regions might be problematic (incorrect) for the following reasons: 1. When I overlay |lh.white| on the original volume, I notice some misregistration (see the figure below). 2. To address this, I applied the |transformationvolume.dat| file generated from |bbregister|, which I used to create the surface with |mri_vol2surface|. However, the transformed |lh.white| surface generated using the |transformationvolume.dat| file appears to be incorrect—it seems to be rotated by 90 degrees (refer to the second figure below). I am unsure what I might be doing wrong. Could you please suggest what mistake I might be making? Thank you once again for your help. Shraddha ------------------------------------------------------------------------ *From:* freesurfer-bounces@nmr.mgh.harvard.edu <mailto:freesurfer-bounces@nmr.mgh.harvard.edu> <freesurfer-bounces@nmr.mgh.harvard.edu> <mailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Fischl, Bruce R.,PHD <BFISCHL@mgh.harvard.edu> <mailto:BFISCHL@mgh.harvard.edu> *Sent:* Friday, December 27, 2024 9:33 AM *To:* Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> <mailto:freesurfer@nmr.mgh.harvard.edu> *Subject:* [External] Re: [Freesurfer] Assistance with mri_vol2surf: Missing Surface Values in Output Hi Shraddha Why do you think the gray regions are a problem? They are just surface locations where the values mapped from the volume are below threshold. You can change the threshold if you bring up the overlay configuration window cheers Bruce *From:* freesurfer-bounces@nmr.mgh.harvard.edu <mailto:freesurfer-bounces@nmr.mgh.harvard.edu> <freesurfer-bounces@nmr.mgh.harvard.edu> <mailto:freesurfer-bounces@nmr.mgh.harvard.edu> *On Behalf Of *Pandey, Shraddha *Sent:* Thursday, December 26, 2024 7:25 PM *To:* Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> <mailto:freesurfer@nmr.mgh.harvard.edu> *Subject:* [Freesurfer] Assistance with mri_vol2surf: Missing Surface Values in Output * External Email - Use Caution * Dear Free Surfer Experts, I am currently working on generating a surface from a volume using the |mri_vol2surf| tool. The process I am following is as follows: 1. I first create the registration file using |bbregister| with the following command: bash bbregister --s "${sub}xx${ses}" --mov "$input_mri" --reg "$output_reg_file" --o "$output_vol_file" --init-header --t1 2. Here, the goal is to generate the |.dat| registration file. 3. Next, I use this |.dat| file in |mri_vol2surf| to generate the surface with the following command: mri_vol2surf --mov "$input_volume" --reg "$output_reg_file" --hemi lh --projfrac 0.2 --o "$output_surface" The input MRI for the |bbregister| command is flash data, and the input volume for |mri_vol2surf| is a paramagnetic volume that has been registered with the Flash data. However, the surface output generated by |mri_vol2surf| contains missing surface values (as shown in the figure below. For instance, the grey regions in the surface estimates). I would greatly appreciate any insights into why this might be occurring and how to resolve the issue. Thank you for your time and assistance! Regards, Shraddha _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://secure-web.cisco.com/1g2zyXq_tSlOwLy4acAPd3j0rcdMg-fsLeRaQRxk7LYqxTvZnDFgu4g3spmOLv-ooZNxsSh2F2fXiA60pC0BU27LjasPAKRuUFZStIc-9DwHZ8IiSt73p3oGfDUkhlg88EbBnURcYepgPrOxU-RpDPtoddlOLLrzCJgjO2Zge9LXK4aWbTRZO1xaVj3tYbQba6fKqlGquU1814zQ6kG7dEQeChec211qJLpol2up4gpcbUp4ZzRH6PzUrr3b4NoWtPM-I--l7KGmdY0iXvwWLMTcCY8v16DbKTiYqIA3MlSOVTo9Enj2AF3PYv677toMhl6aICA3Pznj1a1NdoIABCw/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer>
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