External Email - Use Caution

Hi Douglas,

I'm sorry I did not see the reply. However, according to this FSwiki page (https://secure-web.cisco.com/1ewSiiCxfbK4xZi1tAuiwuw5w7OeKME66LJV0CpSAaOHVvq... , see the information I found below) the transform file should be in the longitudinal directory, if I'm not mistaken. I ran FS 6.0.1 for a previous project and the transform files were present there. Now with FS 7.1.1 they are not present. I ran the recon-all -all -3T pipeline on two different OS and didn't get the needed .lta files.

The transform files are missing for each subject I ran (448) To be sure I've attached the recon-all.log file for the cross, base and longitudinal run for one subject.

Thank you for your help!

Kind regards,

David

cd $SUBJECTS_DIR/<tpid>.long.<baseid>/mri mri_convert -ait transforms/<tpid>_to_<tpid>.long.<baseid>.lta \ -rl $SUBJCECTS_DIR/<tpid>/mri/rawavg.mgz \ -rt nearest -odt uchar \ aseg.mgz aseg-in-rawavg.mgz

Message: 1 Date: Fri, 15 Jan 2021 09:24:33 -0500 From: "Douglas N. Greve" dgreve@mgh.harvard.edu Subject: Re: [Freesurfer] FW: Missing transformation files in longitudinal pipeline To: freesurfer@nmr.mgh.harvard.edu Message-ID: 821a58f9-2fa0-4db1-56fc-75e63c997019@mgh.harvard.edu Content-Type: text/plain; charset="windows-1252"

Are you looking in the base/mri/transforms folder? If it is not there, can you send the recon-all.log file for the base run

On 1/14/2021 11:12 AM, Nederpelt, D. van (David) wrote:

????????External Email - Use Caution

Hi FS-team,

I ran a longitudinal recon-all stream(FS version 7.1.1) ?and trying to convert the aseg.mgz back to native space. However, in the transform file the <tpid>_to_<tpid>.long.<baseid>.lta is missing.

This is the case for every subject I ran, while the recon-all.log showed freesurfer finished without errors. I?ve attached the .log file. The base dir does have the needed transform files.

How can I resolve this and transform ROI to native space?

Thank you in advance,

Kind regards,

David

******************************************* ______________________________________________________ VUmc disclaimer : http://secure-web.cisco.com/1LR8PaInq9faioBV4wOz8RSwnKDDD3kmimYFmZTyHAZ63EeF... AMC disclaimer : http://secure-web.cisco.com/17sYewASoS_ayfu7I7ZppvxN_xtGM_aIVV2MP-PJ1Ab-Gxue...