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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-bounces@nmr.mgh.harvard.edu freesurfer-bounces@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/an 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

External Email - Use Caution

I can, but how will autorecon3 run without finishing autorecon2?

-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@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-bounces@nmr.mgh.harvard.edu freesurfer-bounces@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

you can do -autorecon2 -autorecon3 and it should work. The T2pial is done in the middle of autorecon3. If you don't spec autorecon3, then it will skip the initial part of autorecon3, and that is what is causing the error

On 2/22/19 1:05 PM, Bruce Fischl wrote: 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-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@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.edumailto: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-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@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.edumailto: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.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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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-bounces@nmr.mgh.harvard.edu freesurfer-bounces@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-bounces@nmr.mgh.harvard.edu freesurfer-bounces@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-bounces@nmr.mgh.harvard.edu freesurfer-bounces@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