Hi Jie, Is this a scan of a non-human primate?
Cheers Bruce -----Original Message----- From: freesurfer-boun...@nmr.mgh.harvard.edu <freesurfer-boun...@nmr.mgh.harvard.edu> On Behalf Of Jie Zhao Sent: Thursday, September 3, 2020 9:34 AM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] recon-all error External Email - Use Caution Hi, Bruce I reorineted the views in freesurfer , But the result was wrong again . Please check the figure attached, Is there any problem. BTW, I got the Dicom file, it is .IMA format. How can I use it? Thanks! Jie > -----Original Messages----- > From: "Fischl, Bruce" <bfis...@mgh.harvard.edu> Sent Time: 2020-08-30 > 10:14:46 (Sunday) > To: "Freesurfer support list" <freesurfer@nmr.mgh.harvard.edu> > Cc: > Subject: Re: [Freesurfer] recon-all error > > Hi Jie > > The orientations are incorrect. What freeview thinks is anterior/posterior > (labeled with "A" and "P") is actually inferior/superior. Do you have the > dicoms from this dataset? If not, how was it converted? You need to orient it > properly so it shows correctly in freeview before we will be able to process > it. > > Cheers > Bruce > > ----- > > -----Original Message----- > From: freesurfer-boun...@nmr.mgh.harvard.edu > <freesurfer-boun...@nmr.mgh.harvard.edu> On Behalf Of Jie Zhao > Sent: Saturday, August 29, 2020 10:08 PM > To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> > Subject: Re: [Freesurfer] recon-all error > > External Email - Use Caution > > Here is the snapshot of my freeview window attached. > > > > -----Original Messages----- > > From: "Fischl, Bruce" <bfis...@mgh.harvard.edu> Sent Time: > > 2020-08-30 > > 02:07:50 (Sunday) > > To: "Freesurfer support list" <freesurfer@nmr.mgh.harvard.edu> > > Cc: > > Subject: Re: [Freesurfer] recon-all error > > > > Why do you want to change it? Can you post a snapshot from freeview so we > > can make sure we are on the same page? > > > > -----Original Message----- > > From: freesurfer-boun...@nmr.mgh.harvard.edu > > <freesurfer-boun...@nmr.mgh.harvard.edu> On Behalf Of Jie Zhao > > Sent: Saturday, August 29, 2020 12:25 PM > > To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> > > Subject: Re: [Freesurfer] recon-all error > > > > External Email - Use Caution > > > > Hi Bruce > > > > Thank you for quick answer。 > > > > I tryrd the freeview -v > > /usr/local/freesurfer/subjecs/2018MPRAGE_p4iso.nii, my freeview > > orienatation is RAS. could you tell me how to change it from RAS to > > (ASL)anterior/superior/left. Thanks > > > > Best, > > Jie > > > > > > > > > -----原始邮件----- > > > 发件人: "Fischl, Bruce" <bfis...@mgh.harvard.edu> > > > 发送时间: 2020-08-27 23:39:20 (星期四) > > > 收件人: "Freesurfer support list" <freesurfer@nmr.mgh.harvard.edu> > > > 抄送: > > > 主题: Re: [Freesurfer] recon-all error > > > > > > Hi Jie > > > > > > I would start by looking at your input volume in freeview, my > > > orientation on freeview is RAS. Could you tell me > > > > > > freeview -v /usr/local/freesurfer/subjects/2018MPRAGE_p4iso.nii > > > > > > and make sure that the orientation it displays in is correct (that is, > > > that what freeview thinks is anterior/superior/left are indeed those > > > directions). Usually when we see this type of failure it is because the > > > direction cosines in the input volume are incorrect (typically because > > > the volume was at some point converted to analyze format). Not always, > > > but usually. > > > > > > Cheers > > > Bruce > > > > > > > > > -----Original Message----- > > > From: freesurfer-boun...@nmr.mgh.harvard.edu > > > <freesurfer-boun...@nmr.mgh.harvard.edu> On Behalf Of Jie Zhao > > > Sent: Thursday, August 27, 2020 11:21 AM > > > To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> > > > Subject: Re: [Freesurfer] recon-all error > > > > > > External Email - Use Caution > > > > > > Hi, Andrew > > > > > > Attached is the right recon-all.log file, please check it. > > > I am new to the freesurfer, so really need you advice, Thanks > > > > > > Kind Regards, > > > Jie > > > > > > > > > > -----Original Messages----- > > > > From: "Hoopes, Andrew" <ahoo...@mgh.harvard.edu> Sent Time: > > > > 2020-08-26 > > > > 10:17:00 (Wednesday) > > > > To: "Freesurfer support list" <freesurfer@nmr.mgh.harvard.edu> > > > > Cc: > > > > Subject: Re: [Freesurfer] recon-all error > > > > > > > > Hi Jie, this appears to be the log for your original issue, and not the > > > > talairach registration failure. > > > > Andrew > > > > > > > > On 8/25/20, 9:23 AM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf > > > > of Jie Zhao" <freesurfer-boun...@nmr.mgh.harvard.edu on behalf of > > > > zjuzhao...@zju.edu.cn> wrote: > > > > > > > > External Email - Use Caution > > > > > > > > Hi Andrew > > > > > > > > Thanks fro your response. > > > > I have soruced the Freesurfer. > > > > Attached is the recon-all log. > > > > > > > > Best, > > > > Jie > > > > > > > > > > > > > -----Original Messages----- > > > > > From: "Hoopes, Andrew" <ahoo...@mgh.harvard.edu> > > > > > Sent Time: 2020-08-24 22:22:28 (Monday) > > > > > To: "Freesurfer support list" <freesurfer@nmr.mgh.harvard.edu> > > > > > Cc: > > > > > Subject: Re: [Freesurfer] recon-all error > > > > > > > > > > Hi Jie, > > > > > > > > > > Can you send the subject's full recon-all.log file to provide > > > > some more context for this failure? Usually this error is due to a poor > > > > registration, but there might be something else going wrong here based > > > > on those p values. Have you sourced freesurfer in your environment? > > > > Adding the freesurfer bin dir to your PATH will provide access to > > > > binaries, but there are a few other PATH variables and settings that > > > > get configured by running `source $FREESURFER_HOME/SetUpFreeSurfer.sh`. > > > > > > > > > > best > > > > > Andrew > > > > > > > > > > On 8/24/20, 10:12 AM, "freesurfer-boun...@nmr.mgh.harvard.edu on > > > > behalf of Jie Zhao" <freesurfer-boun...@nmr.mgh.harvard.edu on behalf > > > > of zjuzhao...@zju.edu.cn> wrote: > > > > > > > > > > External Email - Use Caution > > > > > > > > > > Hi, Tim > > > > > > > > > > Thanks for your quick response. > > > > > I set the PATH environment varible to include Freesurfer > > > > binary directory. > > > > > > > > > > I have the new problem when using recon-all , the error is > > > > like this: > > > > > ERROR: talairach_afd: Talairach Transform: > > > > transforms/talairach.xfm ***FAILED*** (p=0.0000, pval=0.0000 < > > > > threshold=0.0050 > > > > > > > > > > How can solve this error? > > > > > > > > > > Regards, > > > > > Jie > > > > > > > > > > > -----原始邮件----- > > > > > > 发件人: "Tim Schäfer" <ts...@rcmd.org> > > > > > > 发送时间: 2020-08-23 16:24:28 (星期日) > > > > > > 收件人: "Freesurfer support list" > > > > <freesurfer@nmr.mgh.harvard.edu> > > > > > > 抄送: > > > > > > 主题: Re: [Freesurfer] recon-all error > > > > > > > > > > > > External Email - Use Caution > > > > > > > > > > > > What happems if you type 'mri_ca_label' in your shell? > > > > > > > > > > > > Did you setup your PATH environment variable to include the > > > > Freesurfer binary directory? > > > > > > > > > > > > Tim > > > > > > > > > > > > > On August 23, 2020 at 9:34 AM Jie Zhao > > > > <zjuzhao...@zju.edu.cn> wrote: > > > > > > > > > > > > > > > > > > > > > External Email - Use Caution > > > > > > > > > > > > > > Dear freesurfer developer: > > > > > > > > > > > > > > I am using Freesurfer 7.1.1 and encounter an error like > > > > this when using recon-all : > > > > > > > > > > > > > > zhao@zhao-VirtualBox:~$ export > > > > SUBJECTS_DIR=/usr/local/freesurfer/subjects > > > > > > > zhao@zhao-VirtualBox:~$ recon-all -s test4 -i > > > > sample-002.nii.gz -autorecon1 > > > > > > > Subject Stamp: > > > > freesurfer-linux-centos6_x86_64-7.1.1-20200723-8b40551 > > > > > > > Current Stamp: > > > > freesurfer-linux-centos6_x86_64-7.1.1-20200723-8b40551 > > > > > > > INFO: SUBJECTS_DIR is /usr/local/freesurfer/subjects > > > > > > > Actual FREESURFER_HOME /usr/local/freesurfer > > > > > > > Linux zhao-VirtualBox 4.15.0-20-generic #21-Ubuntu SMP > > > > Tue Apr 24 06:16:15 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux > > > > > > > Segmentation fault > > > > > > > ERROR: Executable 'mri_ca_label -all-info failed! Is it > > > > missing from the distribution?' > > > > > > > > > > > > > > What can I do to fix this? Thanks > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > Best regards > > > > > > > > > > > > > > Jie Zhao > > > > > > > > > > > > > > > > > > > > > _______________________________________________ > > > > > > > Freesurfer mailing list > > > > > > > Freesurfer@nmr.mgh.harvard.edu > > > > > > > > > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > > > > > > -- > > > > > > Tim Schäfer > > > > > > > > > > > > _______________________________________________ > > > > > > 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 > > > > > > > > > > > > > > > > _______________________________________________ > > > > 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 > > > > _______________________________________________ > > 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