Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30055 discussions

Doing predictive models on freesurfer outputs
by Yunus Soleymani 24 Dec '24

24 Dec '24

External Email - Use Caution Hello FreeSurfer Developers, I have a general statistical question regarding regression models. Our team attempts to create predictive models based on FreeSurfer outputs such as volumes, thicknesses, and curvatures. The predictive variables we are using include several demographic and metabolic factors. We have adjusted our models to account for intracranial volume (ICV) in the population. Instead of simply dividing our outputs by the ICV, we found through our literature review that it is a better approach to include ICV as a covariate alongside our predictive variables in the model. However, we are concerned that including ICV in this manner leads to a significant increase in the R-squared (R²) value of our models due to the effect size provided by ICV. I would like to know whether this is a statistically significant issue, and if it is, how we should address it. Thanks again for your valuable help, Yunus

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Issues with MRI and PET Registration to fsaverage Template
by 문준호 23 Dec '24

23 Dec '24

External Email - Use Caution Hello, I am currently working on registering MRI and PET data from the ADNI dataset, processed using our custom preprocessing pipeline, to the fsaverage template. My goal is to align both the MRI and PET data to the fsaverage template. To achieve this, I followed these steps: *Step 1:* I used mri_coreg to create an LTA file for registering the MRI data to the fsaverage template. Then, I used mri_vol2vol to perform the registration of the MRI data to the fsaverage template. Commands Used: mri_coreg --mov $MRI_PATH --targ $FREESURFER_HOME/subjects/fsaverage/mri/brain.mgz --reg ${OUTPUT_DIR}/mri${num}_reg.lta mri_vol2vol --mov $MRI_PATH --targ $FREESURFER_HOME/subjects/fsaverage/mri/brain.mgz --reg ${OUTPUT_DIR}/mri${num}_reg.lta --o ${OUTPUT_DIR}/mri${num}_to_atlas.nii.gz *Step 2:* I used the LTA file generated in Step 1 and applied mri_vol2vol to register the PET data to the MRI data. Commands Used: mri_vol2vol --mov $PET_PATH --targ ${OUTPUT_DIR}/mri${num}_to_atlas .nii.gz --reg ${OUTPUT_DIR}/mri${num}_reg.lta --o ${OUTPUT_DIR}/pet${num}_to_atlas.nii.gz However, when visualizing the results using Freeview, I noticed that the registration of both the MRI and PET data to the fsaverage template is not accurate. (The MRI and PET data were successfully co-registered.) I have attached some images of the results and the output from the mri_info command for your reference. # Freeview results ## Example 1 [image: image.png] ## Example 2 [image: image.png] ## Example 3 [image: image.png] # mri_info results ## T1w MRI niiRead(): detected input as 64 bit double, reading in as 32 bit float Volume information for {my_mri_data} type: nii dimensions: 128 x 128 x 128 voxel sizes: 1.000000, 1.000000, 1.000000 type: FLOAT (3) fov: 128.000 dof: 1 xstart: -64.0, xend: 64.0 ystart: -64.0, yend: 64.0 zstart: -64.0, zend: 64.0 TR: 0.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 degrees nframes: 1 PhEncDir: UNKNOWN FieldStrength: 0.000000 ras xform present xform info: x_r = -1.0000, y_r = -0.0000, z_r = 0.0000, c_r = -13.0000 : x_a = -0.0000, y_a = 1.0000, z_a = -0.0000, c_a = 16.5000 : x_s = 0.0000, y_s = 0.0000, z_s = 1.0000, c_s = 11.5000 Orientation : LAS Primary Slice Direction: axial voxel to ras transform: -1.0000 -0.0000 0.0000 51.0000 -0.0000 1.0000 -0.0000 -47.5000 0.0000 0.0000 1.0000 -52.5000 0.0000 0.0000 0.0000 1.0000 voxel-to-ras determinant -1 ras to voxel transform: -1.0000 -0.0000 -0.0000 51.0000 -0.0000 1.0000 -0.0000 47.5000 -0.0000 -0.0000 1.0000 52.5000 -0.0000 -0.0000 -0.0000 1.0000 ## brain.mgz Volume information for /usr/local/freesurfer/7.4.1/subjects/fsaverage/mri/brain.mgz type: MGH dimensions: 256 x 256 x 256 voxel sizes: 1.000000, 1.000000, 1.000000 type: UCHAR (0) fov: 256.000 dof: 0 xstart: -128.0, xend: 128.0 ystart: -128.0, yend: 128.0 zstart: -128.0, zend: 128.0 TR: 0.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 degrees nframes: 1 PhEncDir: UNKNOWN FieldStrength: 0.000000 ras xform present xform info: x_r = -1.0000, y_r = 0.0000, z_r = 0.0000, c_r = 0.0000 : x_a = 0.0000, y_a = 0.0000, z_a = 1.0000, c_a = 0.0000 : x_s = 0.0000, y_s = -1.0000, z_s = 0.0000, c_s = 0.0000 talairach xfm : /usr/local/freesurfer/7.4.1/subjects/fsaverage/mri/transforms/talairach.xfm Orientation : LIA Primary Slice Direction: coronal voxel to ras transform: -1.0000 0.0000 0.0000 128.0000 0.0000 0.0000 1.0000 -128.0000 0.0000 -1.0000 0.0000 128.0000 0.0000 0.0000 0.0000 1.0000 voxel-to-ras determinant -1 ras to voxel transform: -1.0000 -0.0000 -0.0000 128.0000 -0.0000 -0.0000 -1.0000 128.0000 -0.0000 1.0000 -0.0000 128.0000 -0.0000 -0.0000 -0.0000 1.0000 Could you please help me identify any potential issues with my approach or the commands I used? I would greatly appreciate any guidance you can provide. Thanks a lot! Best regards, Junho Moon

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preparing config file to run Tracula
by Barletta, Valeria 23 Dec '24

23 Dec '24

Dear Freesurfers, I am setting up the configuration file to run Tracula preproc. I have some doubts on certain variables... * pedir: on my DTI protocol I have "PhaseEncodingDirection": "j-",so I assume it is AP * epifactor : I took it from "EchoTrainLength": 48 * echospacing: shall I take it from "DwellTime": 2.5e-06? In which format should I write it in the file? Thank you, Valeria

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Feature associations between recon-all and synthseg
by Banerjee, Tania 21 Dec '24

21 Dec '24

External Email - Use Caution Hello, I am reaching out to seek guidance on associating brain features generated using SynthSeg (approximately 101 features for the whole brain) with those generated by Recon-All. Given the coarse nature of SynthSeg features, I assume that multiple features from Recon-All might correspond to a single region in SynthSeg. For example, one Synthseg feature is: ctx-lh-caudalmiddlefrontal How can I determine the set of features in recon-all that correspond to this region ctx-lh-caudalmiddlefrontal? Thank you in advance for your time and assistance. Thank you, Tania Banerjee

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Extracting just the eTIV from stats file.
by Zeng, Victor (BIDMC - Keshavan - Psychiatry) 20 Dec '24

20 Dec '24

External Email - Use Caution Hi guys, I need to extract the eTIV from a stats file Its like this: # Measure EstimatedTotalIntraCranialVol, eTIV, Estimated Total Intracranial Volume, 1667606.252292, mm^3 According to https://secure-web.cisco.com/176-9WTUemMQHEI2hQhkubecmphcM6MFO1hfMQO3SLSaZ4…, typing mri_segstats --subject subjid --etiv-only Doesn't work for FS7.1.1. Also the --etiv flag in mri_segstats doesn't seem to work either. And the --etiv flag in asegstats2table. I also tried figuring how its done in recon-all.log but just need the eTIV and no other stats. Whats the best FS command to do this in FS7.1.1? Victor Zeng Beth Israel Deaconess Medical Center PI: Keshavan, Lizano, Bolo -- ---------------------------------------------------------------------- PLEASE NOTE: This message is intended for the use of the person to whom it is addressed. It may contain information that is privileged, confidential and exempt from disclosure under applicable law. If you are not the intended recipient, your use of this message for any purpose is strictly prohibited. If you have received this communication in error, please delete the message and notify the sender so that we may correct our records. See our web page at http://secure-web.cisco.com/1yhjz1Kw9vsKRZdR40nL-BcWzv765EAqKqrY3w1Srb8ikwW… for a full directory of Beth Israel Lahey Health sites, staff, services and career opportunities.

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Help
by Katherine Sawyer 20 Dec '24

20 Dec '24

External Email - Use Caution Hello, When trying to run recon-all I keep getting the following error message: mri_convert: Command not found. ERROR: Executable 'mri_convert -all-info failed! Is it missing from the distribution?' I just wondered what would be causing it and how to fix it? When running initially, I got the error mris_fix_topology: Command not found. My IT department, deleted and reinstalled FreeSurfer and now I am getting the mri_convert error instead. They deleted 7.4.1 and installed 7.4.0 and this issue is now occurring. The commands seem to be missing from the FreeSurfer bin folder for some reason? I am wondering what could be the cause and solution – or if I’m doing something incorrectly. I imagine it is a local problem for me rather than a wider issue. Thank you. Best wishes, Katherine Sawyer

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help
by 黄月虹 20 Dec '24

20 Dec '24

External Email - Use Caution > -----原始邮件----- > 发件人: freesurfer-request(a)nmr.mgh.harvard.edu > 发送时间:2024-12-20 20:43:35 (星期五) > 收件人: huangyuehong(a)stu.hznu.edu.cn > 主题: Welcome to the "Freesurfer" mailing list (Digest mode) > > Welcome to the Freesurfer(a)nmr.mgh.harvard.edu mailing list! > > To post to this list, send your email to: > > freesurfer(a)nmr.mgh.harvard.edu > > General information about the mailing list is at: > > https://secure-web.cisco.com/1swppzx-gPFP5tp-8ifqBZJJEUBqvLwkRhk8kiEa60foCl… > > If you ever want to unsubscribe or change your options (eg, switch to > or from digest mode, change your password, etc.), visit your > subscription page at: > > https://secure-web.cisco.com/1bcCMKQylUb-M5LSlt1J5Omoavz14P715YF9qvRBX66EmE… > > > You can also make such adjustments via email by sending a message to: > > Freesurfer-request(a)nmr.mgh.harvard.edu > > with the word `help' in the subject or body (don't include the > quotes), and you will get back a message with instructions. > > You must know your password to change your options (including changing > the password, itself) or to unsubscribe. It is: > > zoumwove > > Normally, Mailman will remind you of your nmr.mgh.harvard.edu mailing > list passwords once every month, although you can disable this if you > prefer. This reminder will also include instructions on how to > unsubscribe or change your account options. There is also a button on > your options page that will email your current password to you. > The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at https://secure-web.cisco.com/1p5RAyh3XrOw6sVI1Ck5SYeNw6BwVQxZCzFaDAXlXgTsRK… <https://secure-web.cisco.com/1p5RAyh3XrOw6sVI1Ck5SYeNw6BwVQxZCzFaDAXlXgTsRK…> . > Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.

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Fw: Welcome to the "Freesurfer" mailing list (Digest mode)
by 黄月虹 20 Dec '24

20 Dec '24

External Email - Use Caution > -----原始邮件----- > 发件人: freesurfer-request(a)nmr.mgh.harvard.edu > 发送时间:2024-12-20 20:43:35 (星期五) > 收件人: huangyuehong(a)stu.hznu.edu.cn > 主题: Welcome to the "Freesurfer" mailing list (Digest mode) > > Welcome to the Freesurfer(a)nmr.mgh.harvard.edu mailing list! > > To post to this list, send your email to: > > freesurfer(a)nmr.mgh.harvard.edu > > General information about the mailing list is at: > > https://secure-web.cisco.com/19G_vD1R-PUdgNSk-6dsP4CrmgiHrLgcB0Dp1Zo8hH5MKa… > > If you ever want to unsubscribe or change your options (eg, switch to > or from digest mode, change your password, etc.), visit your > subscription page at: > > https://secure-web.cisco.com/1HutEKVL-PtiSBcic7igKoljqCRrwKDzjjkZWKX5gj0t5c… > > > You can also make such adjustments via email by sending a message to: > > Freesurfer-request(a)nmr.mgh.harvard.edu > > with the word `help' in the subject or body (don't include the > quotes), and you will get back a message with instructions. > > You must know your password to change your options (including changing > the password, itself) or to unsubscribe. It is: > > zoumwove > > Normally, Mailman will remind you of your nmr.mgh.harvard.edu mailing > list passwords once every month, although you can disable this if you > prefer. This reminder will also include instructions on how to > unsubscribe or change your account options. There is also a button on > your options page that will email your current password to you. > The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at https://secure-web.cisco.com/1wMY0l8vtjTZjVQnTI7Y9HDtuIA5QahRy5daIdbXO9NY3L… <https://secure-web.cisco.com/1wMY0l8vtjTZjVQnTI7Y9HDtuIA5QahRy5daIdbXO9NY3L…> . > Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.

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mri_convert: Command not found
by Katherine Sawyer 20 Dec '24

20 Dec '24

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obtain vertex neighborhood
by Jiaen Liu 18 Dec '24

18 Dec '24

External Email - Use Caution Hi Freesurfer users I search the FS documents but can't find a way to extract the vertex neighborhood for a particular vertex. I'd like to use data associated with the vertices in the neighborhood. In 3D space, we often use such kernels for filtering. Thanks! Best regards, Jiaen Liu Ph.D. Assistant Professor Advanced Imaging Research Center & Radiology UT Southwestern Medical Center 2201 Inwood Ln Dallas, TX, USA, 75390 Office: 214.645.2750 Website: Liu (Jiaen) Lab | UT Southwestern, Dallas, Texas<https://secure-web.cisco.com/18PydljEg7EKeNzVJZ2fExAIRqZx618rAX7iZIcyZK6dZt…> ________________________________ UT Southwestern Medical Center The future of medicine, today.

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