External Email. Use Caution.

Hi Steph



I think that mri_segstats would work, but I defer to Doug. The output

should be normal volume, viewable in freeview. I'm not sure why you would

want to do this with FA though. Maybe you could give us more details about

what you are trying to accomplish? Seems like you want to project the annot

into the volume, not the FA maps. Not sure if surf2vol takes annots, again

Doug would know



cheers.

Bruce

On Sun, 9 Dec

2018, Winkelbeiner, Stephanie A wrote:



>        External Email - Use Caution

>

> Dear Bruce,

>

> Thanks for your quick and helpful reply!

>

> Using the surface lh.white has worked perfectly.

>

> Do I understand correctly that the output file is the FA volume conform

> with the lh.white surface? Therefore, if I wanted to extract the mean FA

> for each parcel I would use this newly created volume and the annotation

> file? I had previously used mri_segstats, but that wouldn't work here. Is

> that right?

>

> Cheers,

> Steph

>

>

> -----Original Message-----

> From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl

> Sent: Sunday, December 09, 2018 4:48 PM

> To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>

> Subject: [EXTERNAL] Re: [Freesurfer] mri_surf2vol: has many more faces than vertices

>

> External Email. Use Caution.

>

> Hi Stephanie

>

> the -so switch requirees a surface and an overlay. What you have given it is an annotation (NOT a surface) and an overlay. Use one of the surfaces instead (e.g. lh.white)

>

> cheers

> Bruce

>

>

> On Sun, 9 Dec 2018,

> Winkelbeiner, Stephanie A wrote:

>

>>

>>         External Email - Use Caution

>>

>> Hi Freesurfers,

>>

>>  

>>

>> I’m trying to project the surface, a fine-grained parcellation

>> (?h.250.aparc.annot), into volume space (dti_FA) with

>>

>>  

>>

>> for subj in SPN01*; do

>>

>>     if [ -d "${subj}" ];

>>

>>     then

>>

>>         cd $subj/

>>

>> mri_surf2vol \

>>

>> --o FA/annot2FA.nii.gz \

>>

>> --subject $subj \

>>

>> --so $SUBJECTS_DIR/$subj/label/lh.250.aparc.annot

>> $dtipath/$subj/dti_FA.nii.gz

>>

>>                  cd ../

>>

>>                 fi

>>

>> done

>>

>>  

>>

>> However, I get ERROR: MRISread: file

>> ‘$SUBJECTS_DIR/$subj/label/lh.250.aparc.annot’ has more faces than vertices!

>>

>> How can I solve this?

>>

>>  

>>

>> Thanks,

>>

>> Stephanie

>>

>>  

>>

>> Stephanie Winkelbeiner, MSc

>>

>> Research Coordinator

>>

>> Psychiatry Research

>>

>> Zucker Hillside Hospital

>>

>> 75-59 263 Street

>>

>> Glen Oaks, NY 11004

>>

>> Tel: (718) 470-4588

>>

>> Email: swinkelbei@northwell.edu

>>

>>  

>>

>> Northwell Health

>>

>> Visit us at Northwell.edu

>>

>>  

>>

>>

>> The information contained in this electronic e-mail transmission and

>> any attachments are intended only for the use of the individual or

>> entity to whom or to which it is addressed, and may contain

>> information that is privileged, confidential and exempt from

>> disclosure under applicable law. If the reader of this communication

>> is not the intended recipient, or the employee or agent responsible

>> for delivering this communication to the intended recipient, you are

>> hereby notified that any dissemination, distribution, copying or

>> disclosure of this communication and any attachment is strictly prohibited. If you have received this transmission in error, please notify the sender immediately by telephone and electronic mail, and delete the original communication and any attachment from any computer, server or other electronic recording or storage device or medium.

>> Receipt by anyone other than the intended recipient is not a waiver of

>> any attorney-client, physician-patient or other privilege.

>>

>

>

> The information contained in this electronic e-mail transmission and any attachments are intended only for the use of the individual or entity to whom or to which it is addressed, and may contain information that is privileged, confidential and exempt from disclosure under applicable law. If the reader of this communication is not the intended recipient, or the employee or agent responsible for delivering this communication to the intended recipient, you are hereby notified that any dissemination, distribution, copying or disclosure of this communication and any attachment is strictly prohibited. If you have received this transmission in error, please notify the sender immediately by telephone and electronic mail, and delete the original communication and any attachment from any computer, server or other electronic recording or storage device or medium. Receipt by anyone other than the intended recipient is not a waiver of any attorney-client, physician-patient or other privilege.

>

> _______________________________________________

> Freesurfer mailing list

> Freesurfer@nmr.mgh.harvard.edu

> https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.edu_mailman_listinfo_freesurfer&d=DwIDCQ&c=vq5m7Kktb9l80A_wDJ5D-g&r=ycrYUdKGMCyTnsIy5TvOdBwS8HE5ZtmVMesLULEN8xE&m=eM2SEQbkmiooozH7Zm4sEXU3M9v25nIfNB8x0omNTDg&s=woFNJTn2pvVgUniamGCCpAI2W3RP2qSbzLhu5pbw4Yg&e=

>

>

>