[Freesurfer] Importing surface meshes from 3rd party cortical surface reconstruction tools for analysis in fsaverage template space

External Email - Use Caution Hi, I'm working with infant (0-30 month) MR data, and iBEAT ( https://secure-web.cisco.com/1T2WKIelhUu8n_wuNR_5gb37RydVg1xrWEVvlUOdcz2UFWoSKKUO8S38cKClNmhjA13keedLju0Te5qHI70cMu686M8Nz33LUMDSdSc5UQuK9Vnl0b2bAEYY3X2pBwXbzaEnuzeLsX13HY7M0H8yFuJubt2wgqrSe

[Freesurfer] File extension .area failures

h.area and rh.area, but the .area extension is forbidden on the server and the files will not be created. Has anyone ever had issues with an .area extension? Are there any possible workarounds to change the .area extension used by freesurfer? James Bartolotti, Ph.D. (he/him/his) Senior Scientist

[Freesurfer] Postdoctoral Fellowship in Traumatic Brain Injury and Post-traumatic Epilepsy Neuroimaging

traumatic brain injury (TBI) and post-traumatic epilepsy (PTE) neuroimaging to conduct research in advanced quantitative analysis of multimodal neuroimaging data. Successful applicants will be aligned with Andrea Schneider MD PhD and James Gugger MD PharmD, to support related research activities

Re: [Freesurfer] Recon-all failing with pre-skullstripped input data (mri_em_register can't find brainmask.mgz)

t; Hope it helps. > > > > Best, > > > > Yujing > > > > *From:* freesurfer-boun...@nmr.mgh.harvard.edu < > freesurfer-boun...@nmr.mgh.harvard.edu> *On Behalf Of *James Hengenius > *Sent:* Thursday, December 28, 2023 5:06 PM > *To:* Freesurfer support li

[Freesurfer] Recon-all failing with pre-skullstripped input data (mri_em_register can't find brainmask.mgz)

External Email - Use Caution Hello FS experts, I downloaded some anatomical data. I have defaced full images and pre-skullstripped images for each participant. I tried the defaced images first, but FS skullstripping looks a little off (possibly because the defacing hides bits of t

Re: [Freesurfer] 3D printing from freesurfer

External Email - Use Caution You can print from the surfaces. Using mris_convert --combinesurfs $SUBJECTS_DIR/${subject}/surf/lh.pial $SUBJECTS_DIR/${subject}/surf/rh.pial \ $SUBJECTS_DIR/cortical.stl will take the pial surfaces from both hemispheres and combine them

Re: [Freesurfer] FS_7_2_0_ubuntu_198_04_06 root password

External Email - Use Caution Can you send me the password too? I don't have it.

[Freesurfer] Passcode for Archive

A/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FVM_67> Thank you for your time, James Watlington <http://secure-web.cisco.com/1JMdry0mYYRqdCZXgCAgpYd6amucC9yr_uIRr2AOKt91e2yyVjVnBbgYLCba_TcBGsFkWQ9

[Freesurfer] mri_glmfit

ge mri_glmfit: could not scan # of lines from label file I am ot sure what I am doing wrong. Thanks for guidance James ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The informati

Re: [Freesurfer] questions about mri_glmfit

12:22 PM, James Brown wrote: Dear Freesurfer experts, I have 2 questions about the command mri_glmfit and I appreciate your help. 1- Are there any settings or flags that can be used in mri_glmfit to restrict statistical comparison of surface based analysis to specific ROIs rather than whole brain

[Freesurfer] questions about mri_glmfit

adsheet to 8 columns for lobs (frontal, temporal, occipital and parietal) left and right? Also, is there any way to generate a statistical map from the spreadsheet statistics? Thank you and happy holidays :) James ___ Freesurfer mailing list

[Freesurfer] cortical thickness in frontal lobe

tats file under subjid/stats folder. For example, cortical thickness of frontal lobe = sum of frontal parcellates divided by number of parcallates . Do we need to do any correction such as weighing the surface area measurements ? Thank you J

[Freesurfer] Fwd: average lobar cortical thickness

-offset 200 [--base-offset must be last arg] Thank you James ___ 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

[Freesurfer] average lobar cortical thickness

-offset 200 [--base-offset must be last arg] Thank you James ___ 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

Re: [Freesurfer] mri_segment

ation takes two steps! Thank you for pointing this out. I would check your results to see if it is doing the right thing. I also think that the input to mri_segment is not the norm.mgz, but rather the brain.mgz, which is more aggressively normalized On Mon, Oct 24, 2022 at 2:01 PM James Brown wr

Re: [Freesurfer] mri_segment

correct procedure to increase the high limit of WM up to 125 or 140? On Mon, Oct 24, 2022 at 1:46 PM James Brown wrote: > Dear Dr Bruce, Fischl, > > Thank you very much for the detailed explanation. I would like to ask two > additional questions and I highly appreciat

Re: [Freesurfer] mri_segment

the highest limit of white matter intensity in the image is 108? I apologize for asking too many questions. I appreciate the opportunity to learn. Sincerely, James Hi James It really depends on your sequence. Some sequences, like mprage, trade off SNR for CNR, so the distance between

[Freesurfer] mri_segment

ely in the command mri_segment? Does the brightness of the image or motion play a role in the decision of choosing high limits values? Thank you, James ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/f

[Freesurfer] Creating a lobar atlas

e.reg ../label/rh.lobes.annot SUBJECT_TEST rh.my_atlas.gcs I would like to use mri_segstats with “my atlas” to generate statistics in lobes not in parcellates. How can I convert lh.my_atlas.gcs and rh.my_atlas.gcs to myatlas.mgz ? Thanks for yo

Re: [Freesurfer] White matter normalization of FLAIR images

External Email - Use Caution Dear Dr Bruce, Thank you very much for answering my questions and for help. We highly appreciate you. All the best James 1. Sigma is the smoothing kernel applied to the bias field so you can make it pretty large depending on how high frequency

Re: [Freesurfer] White matter normalization of FLAIR images

lization (white/gray and csf) or just white matter normalization within a mask. Thank you very much for all that you do. James it looks like you are using v6. In v6, the flair might not have been normalized  On 9/23/2022 3:53 PM, Fischl, Bruce R.,PHD wrote: I think you need to add somethin

Re: [Freesurfer] White matter normalization of FLAIR images

to normalize FLAIR Sincerely, Hi JamesB there is T2/FLAIR normalization in recon-all if you process it through there. You can look for "nonmax_suppress" if you want to find the command line cheers Bruce On Fri, Sep 23, 2022 at 2:06 PM James Brown wrote: > Dear Freesurfer expe

Re: [Freesurfer] White matter normalization of FLAIR images

feedback about the proper way to correct FLAIR images for bias fields and normalize white matter intensity in FLAIR images. Thank you JamesB On Wed, Sep 21, 2022 at 10:18 AM James Brown wrote: > Dear Freesurfer experts, > In order to normalize white matter intensity of T1 images and cor

[Freesurfer] White matter normalization of FLAIR images

External Email - Use Caution Dear Freesurfer experts, In order to normalize white matter intensity of T1 images and correct for bias field. We do the following steps: mri_convert T1.nii.gz T1.mgz mri_nu_correct.mni --i T1.mgz --o T1_N3.mgz --n 2 mri_normalize -g 1 T1_N3.mgzT1_norm.

Re: [Freesurfer] White matter normalization

External Email - Use Caution Thank you very much for the follow up. I have attached the recon-all.log once again for your kind review Hello James, I apologize that your message containing the log file got rejected. Can you please re-send it? I will manually approve it so

Re: [Freesurfer] White matter normalization

9d8h6L515Zn8JCI-qC1h6XYGUYypkmYk5aJ4XGxrWAwEwV97nVfN9eNbnOSLJ0hXT6mMz9W3_sbOiTe2A3fOoRCRTelL2kBwzKt_Q/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Fconfirm%2Ffreesurfer%2Fc325cabc74fbe917245a011d762c75fc2f62c6ca On Fri, Sep 16, 2022 at 10:25 AM James Brown wrote: > Hi Dr Greeve, > I greatly apologize if I missed in t

Re: [Freesurfer] White matter normalization

essarily be the same normalization that is applied to the t1)  On Mon, Sep 12, 2022 at 4:01 PM James Brown wrote: > Dear Freesurfer experts, > In order to normalize white matter intensity of T1 images and correct for > bias field. I do the following steps: > mri_convert T1.nii.gz T1.mgz

[Freesurfer] White matter normalization

External Email - Use Caution Dear Freesurfer experts, In order to normalize white matter intensity of T1 images and correct for bias field. I do the following steps: mri_convert T1.nii.gz T1.mgz mri_nu_correct.mni --i T1.mgz --o T1_N3.mgz --n 2 mri_normalize -g 1 T1_N3.mgzT1_norm.m

[Freesurfer] Post-doctoral position at University of Pittsburgh in population neuroscience

External Email - Use Caution *Dear All, please see the opportunity for a Post-Doctoral Associate position:* *Link to apply*: Job Description - Post Doctoral Associate (ROSANO) (21008433) (taleo.net)

Re: [Freesurfer] resample_type ignored by mri_convert with --like argument?

External Email - Use Caution Thanks, that worked without error and the resampling looks correct. Jim On Thu, May 12, 2022, 11:42 PM Douglas N. Greve wrote: > Sorry, one more thing. Add --regheader to the command lien > > On 5/12/2022 5:12 PM, James Hengen

Re: [Freesurfer] resample_type ignored by mri_convert with --like argument?

matters. Is mri_vol2vol looking for a Freesurfer generated registration somewhere in the subject directory? Thanks! Jim H On Thu, May 12, 2022 at 3:43 PM Douglas N. Greve wrote: > try this > mri_vol2vol --targ T1w_MNI.nii.gz --interp nearest --mov > ICBM152_2009c_AtlasWhite.nii.gz --o Whi

[Freesurfer] resample_type ignored by mri_convert with --like argument?

External Email - Use Caution Hello FS experts, I'm trying to reslice a third-party atlas into the same resolution as my data in MNI space. I am using the following command: mri_convert --like T1w_MNI.nii.gz --resample_type nearest ICBM152_2009c_AtlasWhite.nii.gz WhiteAtlas_resam

[Freesurfer] Ubuntu developer password

External Email - Use Caution I installed the Ubuntu image in virtual box to run free surfer on windows - can I have the developer user password? Cheers, James. -- *James Allebone | **MPsych, Ph.D. (Clinical Neuropsychology)* Melbourne School of Psychological Sciences The

[Freesurfer] Open positions at The Ohio State University: Post-dococtoral Researcher, Psychometrician, & Study Coordinator

External Email - Use Caution The Clinical Neuroscience Lab, in the Department of Psychology, within the College of Arts and Sciences, seeks a Post-Doctoral Researcher (R29059), a Psychometrician (R13824), and a Study Coodinator (29068) to join our team. The Clinical Neuroscience

[Freesurfer] Subfields error

Mon Aug 16 21:53:27 EDT 2021 -- *James Allebone | **MPsych, Ph.D. (Clinical Neuropsychology)* Melbourne School of Psychological Sciences The University of Melbourne Florey Institute of Neuroscience and Mental Health Melbourne Brain Centre, Austin Campus 245 Burgundy Street, Heidelberg VIC 3084

[Freesurfer] Extracting stats from surface overlay

Neuroscience 25:9, pp. 1477–1492. I would ultimately like to extract average AIs for an ROI analysis. My question is how do I extract the overlay stats from the surface overlay mgh file to obtain average AI in each ROI? Thanks! Jim Gugger James Gugger, MD, PharmD Instructor of Neurology University

[Freesurfer] Superficial white matter surface reconstruction

James Gugger, MD, PharmD Instructor of Neurology University of Pennsylvania ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] recon-all 7.1.1 {Disarmed}

External Email - Use Caution Hi I think i fixed it--just needed to add to PATH correctly in .zprofile Cheers James On Fri, Nov 27, 2020 at 11:16 AM James Hartzell wrote: > Hi Andrew > Hope you're well and safe from Covid. > I've got another problem I hop

Re: [Freesurfer] recon-all 7.1.1 {Disarmed}

or directory Cheers James On Tue, Sep 22, 2020 at 8:40 PM James Hartzell wrote: > Okay, great, thanks Andrew. > I can't think of how (otherwise) I might have known not to do that! > Cheers > James > > On Tue, Sep 22, 2020 at 8:29 PM Hoopes, Andrew > wrote: > >

[Freesurfer] Single Hemisphere Option Availability for Segmentation of hippocampal subfields and nuclei of the amygdala (cross-sectional and longitudinal)

the Hippocampus / Amygdala. Could you let us know if there are any hidden options that enable single hemisphere processing or workflows that allow for this? Thank you so much for your help as always. Sincerely, James Park This e-mail message (including any

[Freesurfer] Support: Password Request for Ubuntu_710 to download Freesurfer on Windows 10 {Disarmed}

External Email - Use Caution Dear Freesurfer Team, Hello, my name is James Park and I have recently been trying to utilize Freesurfer on a new Windows Computer. I was able follow the instructions provided on : https://secure-web.cisco.com

Re: [Freesurfer] [External] Re: Troubleshooting: Question Regarding Copying Freesurfer Output to Secondary Location

External Email - Use Caution Thank you! This has been super helpful. Sincerely, James Park From: freesurfer-boun...@nmr.mgh.harvard.edu Date: Tuesday, October 27, 2020 at 2:21 PM To: Freesurfer support list Subject: Re: [Freesurfer] [External] Re: Troubleshooting: Question

Re: [Freesurfer] [External] Re: Troubleshooting: Question Regarding Copying Freesurfer Output to Secondary Location

you please point me in the right direction as to where I could access more information on rsync or moving data to a different location? That would be super helpful! Thank you again for your help. Sincerely, James Park From: freesurfer-boun

Re: [Freesurfer] [External] Troubleshooting: Question Regarding Copying Freesurfer Output to Secondary Location

External Email - Use Caution Hello, Sorry for the rapid follow up email, I just noticed I left some personal contact information on the previous email. Could you please remove my signature from the archives? Thank you so much. Sincerely, James Park From: freesurfer-boun

Re: [Freesurfer] recon-all 7.1.1

External Email - Use Caution Okay, great, thanks Andrew. I can't think of how (otherwise) I might have known not to do that! Cheers James On Tue, Sep 22, 2020 at 8:29 PM Hoopes, Andrew wrote: > Hi James, please ignore that step. In fact, adding those matlab paths t

Re: [Freesurfer] recon-all 7.1.1

ar/folders/zz/zyxvpxvq6csfxvn_n0/T/tmp.LPxBFTBS/install-target/v84/runtime/maci64:/var/folders/zz/zyxvpxvq6csfxvn_n0/T/tmp.LPxBFTBS/install-target/v84/sys/os/maci64:/var/folders/zz/zyxvpxvq6csfxvn_n0/T/tmp.LPxBFTBS/install-target/v84/bin/maci64:) Cheers James O

Re: [Freesurfer] recon-all 7.1.1

inished mv: rename /var/folders/kl/72rg80dd57ncd7nc638fwzmhgn/T/tmp.0al9EPfQ/install-target/v84 to /Applications/freesurfer/7.1.1/MCRv84: Permission denied Also, if you could provide guidance for the append step, that would be great. Cheers James On Sat, Sep 19, 2020 at 4:17 PM James Hartz

Re: [Freesurfer] recon-all 7.1.1

ii.gz -autorecon1 zsh: permission denied: recon-all zsh: permission denied: recon-all zsh: command not found: zsh: Cheers James On Sat, Sep 19, 2020 at 5:03 PM James Hartzell wrote: > Hi Andrew > > Thanks, cool, that looks like it worked. I'll run recon-all, check the > logs an

Re: [Freesurfer] recon-all 7.1.1

External Email - Use Caution Hi Andrew Thanks, cool, that looks like it worked. I'll run recon-all, check the logs and QA tools and let you know if I come across any issues. Cheers James On Sat, Sep 19, 2020 at 4:36 PM Hoopes, Andrew wrote: > Hi James, > > >

[Freesurfer] recon-all 7.1.1

://raw.githubusercontent.com/freesurfer/freesurfer/fs-7.1/scripts/recon-all > recon-all zsh: permission denied: recon-all Here's hoping you can send another fix! Cheers James -- James Hartzell, PhD (2x) Donostia-San Sebatián, Spain Center for Mind/Brain Sciences (CIMeC), The University of Trento, Italy Ce

Re: [Freesurfer] [External] Re: Troubleshooting -parallel flag for Freesurfer, error in the cortical ribbon mask stage during recon-all

when these changes might formally be incorporated in a later version of freesurfer. Thank you again for your help in advance. Sincerely, James Park From: on behalf of "Douglas N. Greve" Reply-To: Freesurfer support list Date: Tuesday, September 8, 2020 at 6:42 PM To: &

Re: [Freesurfer] [External] Re: Troubleshooting -parallel flag for Freesurfer, error in the cortical ribbon mask stage during recon-all

-darwin-macOS-7.1.1-20200811-8b40551 That would be great thank you so much. Sincerely, James Park From: on behalf of "Douglas N. Greve" Reply-To: Freesurfer support list Date: Tuesday, September 8, 2020 at 12:06 PM To: "freesurfer@nmr.mgh.harvard.edu" Subject: [Exter

Re: [Freesurfer] Troubleshooting -parallel flag for Freesurfer, error in the cortical ribbon mask stage during recon-all

External Email - Use Caution Sincerely, James Park From: "Park, James" Date: Tuesday, September 8, 2020 at 11:48 AM To: "freesurfer@nmr.mgh.harvard.edu" Subject: Troubleshooting -parallel flag for Freesurfer, error in the cortical ribbon mask stage du

[Freesurfer] autorecon2, error MRISreadCurvature:

lh.curv does exist in the subject's surf folder. I ran it twice just to be sure. I don't find an answer for the problem in the freesurfer list. Any guidance will be much appreciated! Cheers James Hartzell, PhD (2x) Donostia-San Sebatián, Spain

[Freesurfer] Network license with user stats

ed in the expected number of users. Is that an acceptable alternative to asking individual to obtain licenses? Also, we can provide detailed usage statistics if there is interest. Thanks, Jim -- James Vincent, PhD BioGrids / SBGrid, Harvard Medical School vinc...@hkl.hms.harvar

Re: [Freesurfer] mris_apply_reg failing for area/volume

External Email - Use Caution Hi Doug Thank you very much for this. I am unfortunately not able to get the new version to work with our system. Is it possible to send a version built for centos6/rhel6? Thanks again! - James From

Re: [Freesurfer] mris_apply_reg failing for area/volume

External Email - Use Caution Thanks for the quick reply. Have sent the file to you now - James From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Greve, Douglas N.,Ph.D. Sent: 07 January 2019 17:42 To: freesurfer@nmr.mgh.harvard.edu

Re: [Freesurfer] mris_apply_reg failing for area/volume

LONG (with another symmetrical template) to show that the error is not template-specific. Thank you in advance! ​- James From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of James Michael Roe Sent: 12 November 2018 10:52 To: Freesurfer support

Re: [Freesurfer] mris_apply_reg failing for area/volume

External Email - Use Caution Hi again Doug FYI have sent the files as requested James From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Greve, Douglas N.,Ph.D. Sent: 08 November 2018 15:01 To: freesurfer@nmr.mgh.harvard.edu

Re: [Freesurfer] mris_apply_reg failing for area/volume

External Email - Use Caution Hi Doug Here is the output file James Michael Roe PhD. Candidate Center for Lifespan Changes in Brain and Cognition Department of Psychology University of Oslo PB 1094 Blindern 0317 Oslo Mobile: 958 49 437

Re: [Freesurfer] mris_apply_reg failing for area/volume

register when using --jac is still unsolved Appreciate the support. Thanks James From: James Michael Roe Sent: 31 October 2018 19:45 To: Freesurfer support list Subject: Re: [Freesurfer] mris_apply_reg failing for area/volume Hi Bruce Can confirm that both

Re: [Freesurfer] mris_apply_reg failing for area/volume

External Email - Use Caution Hi Bruce Can confirm that both files (rh.area & rh.volume) load fine in freeview Thanks for the help! James From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Bruce Fischl Sent: 29 October 201

[Freesurfer] mris_apply_reg failing for area/volume

The error is not template-specific as the output is the same using fsaverage_sym Attached is the log file. Thanks in advance! ?- James subexample_slurm.log Description: subexample_slurm.log ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu

[Freesurfer] Freeview heat map

External Email - Use Caution Dear Freesurfer developers, I analyzed some data in Freesurfer. At the end, I used "mri_segstats" to measure a parameter of interest for every ROI in DKT atlas. I would like to load the mean values of this parameter to Freeview (every ROI in DKT has o

Re: [Freesurfer] SNR for PET images

al Message ‐‐‐ On August 14, 2018 5:07 PM, James Brown wrote: > Hi Freesurfer team, > I would like to use "mri_segstat" to compute SNR for regions of interest. My > question is, if I use PET images as input does this mean that SNR will be > computed for the PET signal in t

[Freesurfer] SNR for PET images

External Email - Use Caution Hi Freesurfer team, I would like to use "mri_segstat" to compute SNR for regions of interest. My question is, if I use PET images as input does this mean that SNR will be computed for the PET signal in the ROIs? Thanks for any help John__

[Freesurfer] Q & A Forum in neuroimaging techniques

n this field. The forum will include chat rooms > and live discussions with an experts in the field. > > We are looking forward for your support and contributions. Please follow us > here: > https://area51.stackexchange.com/proposals/119504/neuroimaging?referrer=JC-

[Freesurfer] Q & A Forum in neuroimaging techniques

ooms and live discussions with an experts in the field. We are looking forward for your support and contributions. Please follow us here: https://area51.stackexchange.com/proposals/119504/neuroimaging?referrer=JC-CieH5cIdCKHgDAqvZmw2 Sincerely, J

Re: [Freesurfer] adding additional manually-defined labels to atlas-derived .annot file

External Email - Use Caution Good Morning All, Just wondering if anyone had any advice regarding this problem? I am still struggling to get things running as intended! Any help would be greatly appreciated. BW James On Tue, Jun 26, 2018 at 1:20 PM, James Hobart wrote: >

[Freesurfer] Resample data for longitudinal comparisons

ecial considerations I need to take into account after the initial recon, or would longitudinal processing after this point be per normal? Thanks, James ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/frees

Re: [Freesurfer] Cortical Thickness at Individual Vertices (fwd)

o: Bruce Fischl > Cc: freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] Cortical Thickness at Individual Vertices > > > External Email - Use Caution > > Hi Bruce! > James: I don't have any particular deep thoughts except, all things equal, > i

[Freesurfer] Cortical Thickness at Individual Vertices

go about that with Freesurfer data? This paper takes a similar approach with DTI. I'd like to do something analogous to their "number of voxels with low FA" analysis. https://www.sciencedirect.com/science/article/pii/S1053811911012146

[Freesurfer] adding additional manually-defined labels to atlas-derived .annot file

? And finally, how do I deal with the fact that the binarymask.label will overlap with other labels? Ideally I need to force the overwrite of vertex labels so that the binarymask.label is prioritised? BW James ___ Freesurfer mailing list Freesurfer

[Freesurfer] Using grad_unwarp

x27;m missing: - create_displacement_tables script - grad_unwarp_converter.pl script - matlab files Is there somewhere I can locate these missing scripts/files? Thanks, James ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu

Re: [Freesurfer] Visualizing Supratentorial volume

mbers and use > mri_binarize with the --match option > > On 5/31/18 3:27 PM, James Gullickson wrote: > > External Email - Use Caution > Sorry I wasn't clear. Yes, I would like to see it with all the non-STV > removed, in order to see exactly what the supratentorial seg

Re: [Freesurfer] Visualizing Supratentorial volume

aseg. > Or do you want all the non-STV removed? If that, you can create a mask > of STV using mri_binarize and --match run on the aseg.mgz, then use > mri_mask aseg.mgz stvmask.mgz aseg-stvonly.mgz > > > > On 05/30/2018 11:56 AM, James Gullickson wrote: > > > > > &g

[Freesurfer] Visualizing Supratentorial volume

analysis. However, I would like to visualize them in my data set for QA purposes to ensure they are capturing what I think they are capturing. Thanks, James ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman

Re: [Freesurfer] Longitudinal data from different sequences and scanners

the same resolution (i.e. using mriconvert)? Also, would a normalized measure like ventricle-brain-ratio theoretically be resistant to these scanner/acquisition induced biases? Thanks, James On Mon, Apr 16, 2018 at 5:15 AM, Martin Reuter wrote: > Hi, > > never switch hardware or proto

[Freesurfer] Brainhack Donosti 2018, San Sebastián, Spain

ality assessment of DWI data Preprocessing data Find your path: tractography and group analysis -- James Hartzell, PhD Basque Center on Cognition, Brain and Language (BCBL), Donostia, Spain Center for Mind/Brain Sciences (CIMeC), The University of Trento, Italy Center

[Freesurfer] Abstract submission deadline extended - 1st International Workshop on Predictive Processing

://www.bcbl.eu/events/prediction-2018/en/ We look forward to seeing you at the conference. Yours sincerely, The Organizing Committee Manuel Carreiras, Clara Martin, Nicola Molinaro & David Soto -- James Hartzell, PhD Basque Center on Cognition, Brain and Language (BCBL), Donostia, Spain Ce

Re: [Freesurfer] Longitudinal data from different sequences and scanners

All, Just wanted to follow up on this message. Does anyone have recommendations for the best way to compare this data longitudinally? Thanks very much, James On Thu, Mar 29, 2018 at 1:19 PM, James Gullickson wrote: > All, > > Our lab is working with longitudinal (two time points) da

[Freesurfer] Longitudinal data from different sequences and scanners

then bringing each image into the halfway space between the two (as FSL's SIENA does). Thanks, James ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e

[Freesurfer] Qdec question when examining group differences with continuous covariate and nuisance factor

account for this? Mean ICV values are almost identitical between groups. Or is there some additive affect at the cluster level? Many thanks for any clarity you can provide. Kind regards, James ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https

[Freesurfer] Masking cortical thickness

full recon-all s for these cases. I was thinking I would need to mask the cortical thickness map somehow (potentially mapping the mask volume to a surface?) before using the mris_anatomical_stats to calculate cortical thickness. Is this the best way to go about this? Many thanks James

Re: [Freesurfer] motion estimates

want to do it manually. freeview can help with this - draw ROIs in the gray and white matter, then look at the difference between the means (squared) divided by the sum of the variance On Thu, 31 Aug 2017, James Welsh wrote: > > Thank you Dr Bruce for the info! Is this command works on T1

Re: [Freesurfer] motion estimates

Subject: Re: [Freesurfer] motion estimates Hi James after running recon-all you can use mri_cnr to measure CNR (which is usually more interesting than SNR). Motion is harder. Martin investigated this at some point, but I'm not sure where he left it cheers Bruce On Thu, 31 Aug 2017, James Welsh

[Freesurfer] motion estimates

Dear Freesurfer experts, I want to inquire if there are any tools in freesurfer that can help to evaluate T1 quality regarding motion and SNR. Thanks! James ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu

Re: [Freesurfer] recon-all on T1s without anterior coil

image as an example). I will have to try it with anterior control points on and see if we get a better result. In the end, it looks like we may just have to bring this subject back in to re-do the scan. Thanks! James On Sun, Jun 11, 2017 at 6:50 PM, Bruce Fischl wrote: > Hi James > >

[Freesurfer] recon-all on T1s without anterior coil

lost cause at this point? Thanks, James Gullickson ___ 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

Re: [Freesurfer] illustration of a nifti volume on fsaverage

Thank you Bruce. What if the nifti volume has not been processed at all in Freesurfer? My only aim is to illustrate an overlay on FSAVERAGE, with the obvious caveat of skipping surface construction for this nifti. Thanks, James On Tue, May 9, 2017 at 2:42 PM, Bruce Fischl wrote: > if the ni

[Freesurfer] illustration of a nifti volume on fsaverage

m not sure what tools from Freesurfer I should use for 1) between subject volume registration (nifti volume to fsaverage volume) 2) fsaverage volume to fsaverage surface. Thank you, James ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu

[Freesurfer] cortex parcellation

what pathology these subjects have? Where can I find these? Thank you, James Pardon ___ 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

Re: [Freesurfer] Ventricle-to-Brain Ratio

Doug, Thank you very much! That helps clear things up for me. Best, James On Mon, Apr 10, 2017 at 2:21 PM, Douglas N Greve wrote: > sorry, I would use these two > > TVV = left lateral ventricle + left inf lateral ventricle + right > lateral ventricle + right inf lateral ven

Re: [Freesurfer] Ventricle-to-Brain Ratio

Hi Doug, To clarify: to calculate VBR, I need two things: a measure of TBV *and* and measure of TVV. I'm just wondering what the best way to derive each of these is. Thanks, James On Fri, Apr 7, 2017 at 11:24 AM, Douglas N Greve wrote: > I would use the TVV > > > On 04

Re: [Freesurfer] Ventricle-to-Brain Ratio

representation of total brain volume (all parenchyma) Best, James On Thu, Apr 6, 2017 at 3:17 PM, Douglas N Greve wrote: > that looks right. how different are the values? > > > On 04/05/2017 10:58 AM, Gullickson, James wrote: > > Hello all, > > > > I want to calculate a Ven

[Freesurfer] Ventricle-to-Brain Ratio

- BrainSegVolNotVent and for TBV TBV = TotalGrayVol + CorticalWhiteMatterVol which differs from TBV = BrainSegVolNotVent Thank you for your help, James Gullickson ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu

[Freesurfer] Multiple Frames Error

Hello, I’ve been having a problem with recon-all lately. I’m relatively new to FreeSurfer and the processes that I have done in the past have been done on sample individualized scans in my lab and I ran into an issue once I started trying to run FreeSurfer on fMRI data provided by our lab. Whene

[Freesurfer] Error w/ recon-all

running at one point but died in an unexpected way. If it is the case that there is a process running, you can kill it and start over or just let it run. If the process has died, you should type: rm /export/home/jawilks/freesurfer/subjects/run_02/scripts/IsRunning.lh+rh and re-run. Or you

Re: [Freesurfer] fsaverage_sym LR-flipchecks

du Subject: Re: [Freesurfer] fsaverage_sym LR-flipchecks Sorry, what are you trying to do? What did you do before you ran isxconcat? What was your isxconcat command line? On 11/18/2016 11:34 AM, James Roe wrote: > Thanks for your reply, Doug. Registering both LH and RH to fsaverage_sym > wo

Re: [Freesurfer] fsaverage_sym LR-flipchecks

1st level analyses in the average template spaces? Thanks! James > On 1. nov. 2016, at 18.33, Douglas N Greve wrote: > > But how did you do the analysis on fsaverage_sym? Not that you cannot > just supply fsaverage_sym to preproc-sess. It is unfortunately much more > complicated

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