External Email - Use Caution
Hi,
I’m also encountering a similar issue. I am using Freesurfer 6.0.0 with the
new recon-all.makefile copied in. After completing manual edits, I re-ran
the recon with the -make all flag. The recon-all.log for this subject
indicates that the recon fi
External Email - Use Caution
Hi all,
Just following up on this as I've run into the exact same problem. Is there
a different recon-all.makefile that should be used for FS 6/6.0.1 ?
Thanks!
On Fri, Mar 29, 2019 at 9:28 AM Matthieu VANHOUTTE <
matthieuvanhou...@gmail.com> wrote:
surfer@nmr.mgh.harvard.edu>>
*Subject: *[Freesurfer] Error with recon-all: You are trying
to re-run an existing subject with (possibly) new input data
(-i).
*External Email - Use Caution *
Dear all,
I am trying to run recon-all command for a
t;
>>
>>
>> rm -rf $SUBJECTS_DIR/ben
>>
>>
>>
>> Should clear the issue.
>>
>>
>>
>> best
>>
>> Andrew
>>
>>
>>
>>
>>
>> *From: * on behalf of Peng Liu <
>> claud
ehalf of Peng
Liu mailto:claudialiu1...@gmail.com>>
*Reply-To: *FS Help mailto:freesurfer@nmr.mgh.harvard.edu>>
*Date: *Friday, March 20, 2020 at 6:39 AM
*To: *FS Help mailto:freesurfer@nmr.mgh.harvard.edu>>
*Subject: *[Freesurfer] Error with recon-all: You are trying to
re
> Should clear the issue.
>
>
>
> best
>
> Andrew
>
>
>
>
>
> *From: * on behalf of Peng Liu <
> claudialiu1...@gmail.com>
> *Reply-To: *FS Help
> *Date: *Friday, March 20, 2020 at 6:39 AM
> *To: *FS Help
> *Subject: *[Freesurfer] Erro
Hi Peng,
Are you sure you’re deleting the subject folder from within the SUBJECTS_DIR?
rm -rf $SUBJECTS_DIR/ben
Should clear the issue.
best
Andrew
From: on behalf of Peng Liu
Reply-To: FS Help
Date: Friday, March 20, 2020 at 6:39 AM
To: FS Help
Subject: [Freesurfer] Error with recon
External Email - Use Caution
Dear all,
I am trying to run recon-all command for a subject ben. Before I perform
this command, I have exported SUBJECTS_DIR to a folder with only T1 data
for this subject ben in it. However after I entered the command "recon-all
-s ben -i T1.nii -all
External Email - Use Caution
Dear Freesurfer's experts,
Havng done multiple types of manual editing in two subjects, I
relaunched the recon-all process (Freesurfer 6.0.1) with the flag "-make
all".
However, during the process, I goth for both subjects the following
error mess
Hi Martin,
Thanks for your suggestion, I will try rerunning the base from scratch to see
if this makes a difference. With regards to the base and time-point IDs, those
included in the files I sent you were actually not the IDs we use. I did a find
and replace to remove our actual IDs in case t
Hi Bronwyn,
I would guess that there has been a problem with the way you run the base.
Take one case, copy the cross sectionals into a new directory and re-run
the base from scratch.
If your two time points are named like: TPID_001 and TPID_002 then the
base command should be:
recon-all -b
Hi Bronwyn
I defer to Martin :)
Bruce
On Fri, 18 Aug 2017, Bronwyn Overs wrote:
Hi Bruce,
Please find attached both the command line output and the recon-all log. The
command line I ran was:
recon-all -long BASEID_001 TPID_001 -all
I have already run and reviewed the cross-sectional and base
Hi Bronwyn
can you send us the full command line you ran, screen output and
recon-all.log? And maybe a description of where you are in the process?
You already ran all the tps through the cross? And created the base?
cheers
Bruce
On Thu,
17 Aug 2017, Bronwyn Overs wrote:
Hi again list,
So
Hi again list,
Sorry I made a mistake. The lh.sphere.reg and lh.smoothwm are both in the base
image directory, but I’m still receiving the mismatch error. Partial ls -l
displayed below:
[b.overs@katana surf]$ ls -l $SUBJECTS_DIR/BASEID_001/surf
total 120260
...
-rw-rw-r-- 1 b.overs GroupID 4554
Dear freesurfer mailing list,
I have been running the recon-all -long command and received the following
errors:
#
#@# Surf Reg lh Wed Aug 16 18:07:26 AEST 2017
/mridata/workingdata/CHD/BAR/PROCESSING/longitudinal.fix/TPID_001.long.BASEID_001/scripts
are you looking in the right place? Look in $SUBJECTS_DIR, not the
current directory
doug
On 8/5/13 5:45 PM, Joseph Andreano wrote:
> Hi All,
>
> I'm trying to use recon-all on some structural data, and when I drop the
> command (specifically, recon-all -i
> /cluster/iaslab/SPAR/mri/recon/3dana
Hi Joe
try adding -all to the end. You need to specify a directive for it to
carry out
cheers
Bruce
On Mon, 5 Aug 2013, Joseph Andreano wrote:
> Hi All,
>
> I'm trying to use recon-all on some structural data, and when I drop the
> command (specifically, recon-all -i
> /cluster/iaslab/SPAR/mri/
Hi All,
I'm trying to use recon-all on some structural data, and when I drop the
command (specifically, recon-all -i
/cluster/iaslab/SPAR/mri/recon/3danat/003/001.mgz -subjid
SPAR_016_130708), I get this error message:
ERROR: You are trying to re-run an existing subject with (possibly) new
input
it looks like someone accidentally turn on jpeg compression on the
console. Our converter does not read jpeg. You can use dcmdjpeg from the
dcmtk toolkit to create new dicoms that are uncompressed, something like
dcmdjpeg +te old.dcm new.dcm
doug
On 07/30/2012 01:00 PM, Nathan Hutcheson wrot
I am trying to import an MPRAGE structural sequence of 160 images acquired
from a Siemens Allegro. Only one of my subjects displays the following
error message when I try to import him using the "recon-all -s Subject -i"
function. Below is the brief error message and full log. Thanks in advance
for
the memory requirements of the topo fixer are quadratic in the convex
hull of the largest defect, so check the lh.orig.nofix and see if there is
a connection to the skull or the cerebellum. You will probably need to fix
it in the wm.mgz
cheers
Bruce
On Thu, 10 May 2012, Ed
Gronenschild wrote
Hi Nick,
Apologies, I should have looked at the recon-all.log file
myself. It says that there was an error with mris_topo_fixer:
it couldn't allocate memory (malloc error). So I guess that
the brainmask is still not correct. I will try to fix that with
the option -wsmore.
Cheers,
Ed
On 9 May 201
Hi,
I'm using the version of recon-all that Nick provided
at April 17 to be able to run nu_correct prior to the
Talairach stage. (I'm on a Mac, OSX 10.6, version
v5.1.0). The command given was
recon-all -autorecon-all -hippo-subfileds -no-wsgcaatlas \
-clean-tal -s subject.
recon-all stopped and
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