What version of FS are you running? That flag was introduced with v6
On 6/1/2020 12:57 PM, Mason Wells wrote:
External Email - Use Caution
Hi Doug,
That flag isn’t recognised in the terminal? Have I placed the flag in the wrong place? I tried it between the –feat and the directory, same outcome.
bbregister --s PPT_001 --feat /cubric/data/c1749990/PhD/Data/PMA_retinoScans/PPT_001/run1_pre_processed_functional.feat/ --int /cubric/data/c1749990/PhD/Data/PMA_retinoScans/PPT_001/WholeEPI.nii.gz --init-header --init-coreg
ERROR: Flag --init-coreg unrecognized.
--s PPT_001 --feat /cubric/data/c1749990/PhD/Data/PMA_retinoScans/PPT_001/run1_pre_processed_
*Mason T Wells, MSc*
*PhD student*
School of Optometry and Vision Sciences
& Cardiff University Brain Research
Imaging Centre (CUBRIC), School of Psychology
Cardiff University
Cardiff
CF24 4HQ
UK
*/Email/*: WellsMT1@cardiff.ac.uk mailto:WellsMT1@cardiff.ac.uk
*/Tel/*: 02920 879628
*/Web/*: Cardiff University webpage https://www.cardiff.ac.uk/people/research-students/view/974214-
*Mason T Wells, MSc*
*Myfyriwr PhD*
Yr Ysgol Optometreg a Gwyddorau’r Golwg
& Canolfan Ymchwil Delweddu’r Ymennydd Prifysgol Caerdydd (CUBRIC), Yr Ysgol Seicoleg
Prifysgol Caerdydd
Heol Maindy
Caerdydd
CF24 4HQ
DU
*/E-bost/*: WellsMT1@caerdydd.ac.uk mailto:WellsMT1@caerdydd.ac.uk
*/Ffôn/*: 02920 879628
*From: *freesurfer-bounces@nmr.mgh.harvard.edu on behalf of "Douglas N. Greve" dgreve@mgh.harvard.edu *Reply to: *Freesurfer support list freesurfer@nmr.mgh.harvard.edu *Date: *Monday, 1 June 2020 at 17:38 *To: *"freesurfer@nmr.mgh.harvard.edu" freesurfer@nmr.mgh.harvard.edu *Subject: *Re: [Freesurfer] Bbregister misalignment
Sorry for missing your first email. Can you try adding --init-coreg to your first bbregister command? Make sure to add it AFTER --feat
On 6/1/2020 12:06 PM, Mason Wells wrote:
* External Email - Use Caution * Hi Experts, I posted earlier, but I believe my message has not been posted due to the size of attachments so I’ve removed them. I am using bbregister to align functional data to anatomical space. I have been using the bbregister command with a combination of different flags. However, there appears to be varying levels of poor registration. The first command I used included flags for a whole brain ref image and the --init-header flag. This leads to a misalignment. bbregister --s PPT_1x --feat /Data/PMA_retinoScans/PPT_1x/run1_pre_processed_functional.feat/ --int Data/PMA_retinoScans/PPT_1x/WholeEPI.nii.gz --init-header I then removed the –int (whole brain reg image) flag. Again the registration is massively misaligned. bbregister --s PPT_1x --feat /Data/PMA_retinoScans/PPT_1x/run1_pre_processed_functional.feat --init-header I then removed the –init-header flag. Again poor registration. Then I removed both flags. This was the best registration, but even this still looks a little bit off to me. You can see that around the occipital lobe (reg3 attached), there white matter isn't aligned very well. bbregister --s PPT_1x --feat /Data/PPT_1x/run1_pre_processed_functional.feat/ Can anyone give me any advice on this? I really am unsure as to which why these flags failed to aid registration. I have 3 other participants from a different dataset for which the bbregister pointing to the feat directory *and *the –init-header flag worked perfectly. Have I missed an important step that could explain why no combination seems to register the data correctly? Any advice would be great. Thanks in advance, Mason *Mason T Wells, MSc* *PhD student* School of Optometry and Vision Sciences & Cardiff University Brain Research Imaging Centre (CUBRIC), School of Psychology Cardiff University Cardiff CF24 4HQ UK */Email/*: WellsMT1@cardiff.ac.uk <mailto:WellsMT1@cardiff.ac.uk> */Tel/*: 02920 879628 */Web/*: Cardiff University webpage <https://www.cardiff.ac.uk/people/research-students/view/974214-> *Mason T Wells, MSc* *Myfyriwr PhD* Yr Ysgol Optometreg a Gwyddorau’r Golwg & Canolfan Ymchwil Delweddu’r Ymennydd Prifysgol Caerdydd (CUBRIC), Yr Ysgol Seicoleg Prifysgol Caerdydd Heol Maindy Caerdydd CF24 4HQ DU */E-bost/*: WellsMT1@caerdydd.ac.uk <mailto:WellsMT1@caerdydd.ac.uk> */Ffôn/*: 02920 879628 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> *MailScanner has detected a possible fraud attempt from "eur03.safelinks.protection.outlook.com" claiming to be* https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer&data=02%7C01%7CWellsMT1%40cardiff.ac.uk%7C07a8aefd19a7451b8cf008d8064a262b%7Cbdb74b3095684856bdbf06759778fcbc%7C1%7C0%7C637266262822312923&sdata=byrLRqw8%2BG%2F9xn6f2MPRyhf88YG4DPT%2FkvNvM0SSrrg%3D&reserved=0>
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