External Email - Use Caution But that's the problem. Autorecon2 won't finish because it's looking for lh.white, and it's not being made. I tried to run just "recon-all -white" to see if that would create it, and it still didn't.
-----Original Message----- From: freesurfer-boun...@nmr.mgh.harvard.edu <freesurfer-boun...@nmr.mgh.harvard.edu> On Behalf Of Bruce Fischl Sent: Friday, February 22, 2019 12:06 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] ?h.white does not exist no, you need to run autorecon2 first On Fri, 22 Feb 2019, Weber, Wade A wrote: > External Email - Use Caution > > I can, but how will autorecon3 run without finishing autorecon2? > > -----Original Message----- > From: freesurfer-boun...@nmr.mgh.harvard.edu > <freesurfer-boun...@nmr.mgh.harvard.edu> On Behalf Of Bruce Fischl > Sent: Friday, February 22, 2019 11:58 AM > To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> > Subject: Re: [Freesurfer] ?h.white does not exist > > Hi Wade > > I don't think you can just skip autorecon3. Can you try running it first and > see if that fixes your problems? > > cheers > Bruce > On Fri, 22 Feb 2019, Weber, Wade A > wrote: > >> External Email - Use Caution >> >> Hi Bruce, >> >> I'm using MPRAGEs that aren't as FreeSurfer friendly as they could be, so I >> have to do some Pial edits. So I just skip autorecon3 to save time. After >> I finish the edits, I re-run from -autorecon-pial and check again. Then I >> run autorecon3. >> >> Wade >> >> >> -----Original Message----- >> From: freesurfer-boun...@nmr.mgh.harvard.edu >> <freesurfer-boun...@nmr.mgh.harvard.edu> On Behalf Of Bruce Fischl >> Sent: Friday, February 22, 2019 11:38 AM >> To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> >> Subject: Re: [Freesurfer] ?h.white does not exist >> >> Hi Wade >> >> from the recon-all.log it looks like you never ran autorecon3. Is >> there a reason for this? Usually we run all the way through >> autorecon3 before running the T2pial stuff >> >> cheers >> Bruce >> On Fri, 22 Feb 2019, Weber, Wade A wrote: >> >>> >>> External Email - Use Caution >>> >>> Hi all, >>> >>> >>> >>> I’m trying to run –autorecon2 on 3 subjects (I already ran >>> –autorecon1 on them with no errors.) and I’m getting an error after >>> the –final_surfs part saying that lh.white does not exits (and it >>> doesn’t, I checked for it). I have run about 10 other subjects, and they >>> all ran fine and contain ?h.white files. I saw 2 other strings in the >>> archive with this same issue, but there was no resolution to them. >>> This error just started happening, and I didn’t change anything. Here’s >>> the command I’ve been using: >>> >>> >>> >>> recon-all –subjid <my subject #> -T2 <name of t2.nii file> -T2pial >>> -autorecon2 >>> >>> >>> >>> Here’s the error output: >>> >>> >>> >>> MRISread(/home/waw758/Desktop/secure/Mbemba/Mbemba_freesurfer_stuff/ >>> a >>> n >>> alysis_files/ANG_1034/surf/lh.wh >>> ite): could not open file >>> >>> >>> >>> I’m running >>> freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c >>> on a virtual machine running Red Hat Enterprise Linux Workstation >>> 7.6 >>> >>> >>> >>> I’ve attached the recon-all.log file >>> >>> >>> >>> Thanks! >>> >>> >>> >>> >>> >>> ---- >>> >>> >>> >>> Wade A. Weber, MS >>> >>> Psychiatry Research Program Coordinator >>> >>> >>> >>> Dell Medical School | The University of Texas at Austin >>> >>> o: 512-495-5217 | f: 512-495-5482 | dellmedschool.utexas.edu >>> >>> >>> >>> >>> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
