Re: [Freesurfer] 6.0 release date?
Okay, thank you! Cheers, Renata On Thu, Dec 15, 2016 at 5:09 PM, Bruce Fischl <fis...@nmr.mgh.harvard.edu> wrote: > Hi Renata > > > we are hoping it goes out in either late Dec or early-to-mid Jan, but of > course it depends on it passing lots of tests, so we can't say for sure > > cheers > Bruce > > > On Thu, 15 > Dec 2016, Vaz pandolfo, Renata wrote: > > > Dear FS experts, > > > > My colleagues and I are planning some projects and we were wondering if > > there are any news on the release date of the FreeSurfer 6.0 stable > version. > > We noticed that there was a new developmental version released today, is > > that good news? > > > > An approximation of whether it will be a matter of weeks or months would > > suffice. > > > > Thank you! > > > > Renata > > > > > > > > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > The information in this e-mail is intended only for the person to whom it > is > addressed. If you believe this e-mail was sent to you in error and the > e-mail > contains patient information, please contact the Partners Compliance > HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. > > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] 6.0 release date?
Awesome, thanks! Cheers, Renata On Thu, Dec 15, 2016 at 5:15 PM, Douglas N Greve <gr...@nmr.mgh.harvard.edu> wrote: > We actually have a tentative date of Dec 21 (next Wednesday!). In the > middle of testing now > > > On 12/15/2016 11:09 AM, Bruce Fischl wrote: > > Hi Renata > > > > > > we are hoping it goes out in either late Dec or early-to-mid Jan, but of > > course it depends on it passing lots of tests, so we can't say for sure > > > > cheers > > Bruce > > > > > > On Thu, 15 > > Dec 2016, Vaz pandolfo, Renata wrote: > > > >> Dear FS experts, > >> > >> My colleagues and I are planning some projects and we were wondering if > >> there are any news on the release date of the FreeSurfer 6.0 stable > version. > >> We noticed that there was a new developmental version released today, is > >> that good news? > >> > >> An approximation of whether it will be a matter of weeks or months would > >> suffice. > >> > >> Thank you! > >> > >> Renata > >> > >> > >> > >> > > ___ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > gr...@nmr.mgh.harvard.edu > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > The information in this e-mail is intended only for the person to whom it > is > addressed. If you believe this e-mail was sent to you in error and the > e-mail > contains patient information, please contact the Partners Compliance > HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. > > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] 6.0 release date?
Dear FS experts, My colleagues and I are planning some projects and we were wondering if there are any news on the release date of the FreeSurfer 6.0 stable version. We noticed that there was a new developmental version released today, is that good news? An approximation of whether it will be a matter of weeks or months would suffice. Thank you! Renata ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] FoV in additional scan
Okay, thanks! Best, Renata On Mon, Sep 19, 2016 at 3:34 PM, Iglesias Gonzalez, Eugenio < e.igles...@ucl.ac.uk> wrote: > Hi Renate, > as long as the additional scan is more or less aligned with the T1 in > physical coordinates (i.e., they appear decently aligned when you open them > in Freeview), you should be fine and not need to do anything. > Cheers, > /E > > Juan Eugenio Iglesias > Senior Research Fellow > Translational Imaging Group > University College London > http://www.jeiglesias.com > http://cmictig.cs.ucl.ac.uk/ > > > On 19 Sep 2016, at 14:31, Vaz pandolfo, Renata <r...@njit.edu> wrote: > > Dear Eugenio, > > We have another question about the Hippo Sf Segmentation with an > additional scan. > > Some of our additional scans (FLAIRs or T2s) have a bigger field of view > as compared to the T1 (ex.: they cover more of the neck almost up to the > shoulders of the subjects, while the T1 has the "normal" FoV). > > Should the additional scan be cropped or preprocessed in any way (ex.: > bias field correction)? And if so, should we process the T1 in the same > way or is it generally recommended to just use the raw images? > > Thank you! > > Renata > > > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] FoV in additional scan
Dear Eugenio, We have another question about the Hippo Sf Segmentation with an additional scan. Some of our additional scans (FLAIRs or T2s) have a bigger field of view as compared to the T1 (ex.: they cover more of the neck almost up to the shoulders of the subjects, while the T1 has the "normal" FoV). Should the additional scan be cropped or preprocessed in any way (ex.: bias field correction)? And if so, should we process the T1 in the same way or is it generally recommended to just use the raw images? Thank you! Renata ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] FLAIR for hippo subfield segmentation with an additional scan
Dear Jorge, In my case I am using either T1+T2 or T1+FLAIR. I had no intention of using all three at once, but now I am also wondering if this would be an improvement. Cheers, Renata On Mon, Sep 5, 2016 at 4:54 PM, Jovicich, Jorge <jorge.jovic...@unitn.it> wrote: > Hi Eugenio, > > just to confirm I understand the currently available options. There are > two multispectral strategies (MPRAGE + high res 2D T2, or MPRAGE + 3D > FLAIR). It would be great to see if the combo option improves things even > further for the subfields (MPRAGE + high res 2D T2 + 3D FLAIR). Is that > option at all possible with the available FS version or in the works? > > Best, > > Jorge > > On 05/09/2016 16:13, Iglesias, Eugenio wrote: > > The same one; just change the input file and the analysis ID > > - T2: recon-all -s mySubject -hippocampal-subfields-T1T2 > myT2scan.nii.gz T2 > > - FLAIR: recon-all -s mySubject -hippocampal-subfields-T1T2 > myFLAIRscan.nii.gz FLAIR > > Cheers, > > /Eugenio > > Juan Eugenio Iglesias > Senior Research Fellow > Translational Imaging Group > University College London > http://www.jeiglesias.com > http://cmictig.cs.ucl.ac.uk/ > > > On 5 Sep 2016, at 15:10, Vaz pandolfo, Renata <r...@njit.edu> wrote: > > Dear FS experts, > > > I have a question about the "segmentation with an additional scan - > multispectral segmentation" > on the hippocampal sf segmentation, FS dev. 6.0. > > For controls on which I had already run recon-all -all, I added the T2 > sequence with the following > command: > > recon-all -s \ > -hippocampal-subfields-T1T2 > > > Now, if I want to do the same thing with FLAIR as the additional input, which > flag should I use? > > Thank you, > > Renata > > > > > ___ > Freesurfer mailing > listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > The information in this e-mail is intended only for the person to whom it is > addressed. If you believe this e-mail was sent to you in error and the e-mail > contains patient information, please contact the Partners Compliance HelpLine > athttp://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. > > > -- > Jorge Jovicich, Ph.D. > > MR Lab Head > Center for Mind/Brain Sciences > University of Trento, > Via delle Regole, 101 > 38100 Mattarello (TN) > Italy > > Telephone: +39-0461-28 3064 > Fax: +39-0461-28-3066 > Email: jorge.jovic...@unitn.it > MRI Methods Group: http://r.unitn.it/en/cimec/mri > CIMEC: http://www.cimec.unitn.it/ > > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] FLAIR for hippo subfield segmentation with an additional scan
Dear FS experts, I have a question about the "segmentation with an additional scan - multispectral segmentation" on the hippocampal sf segmentation, FS dev. 6.0. For controls on which I had already run recon-all -all, I added the T2 sequence with the following command: recon-all -s \ -hippocampal-subfields-T1T2 Now, if I want to do the same thing with FLAIR as the additional input, which flag should I use? Thank you, Renata ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] hippo sf segmentation 6.0 dev
Dear Eugenio, I have a couple of questions regarding the hippocampus subfields segmentation on the dev FS 6.0 which I hope you could help me with. We are comparing the volumes of hippocampal subregions of patients and controls, and we would like to be as consistent as possible with the input so that the output reflects only the differences we expect to see. The problem is that we have a large number of controls but not all of them have the same sequences (T1, T2 or FLAIR) as the patients. So our questions are: If the T1s from some subjects have a 1x1x1 resolution and others have 0.8x0.8x0.8 isotropic resolution, do we have to create two groups of controls and patients for each sequence? In other words, does the resolution of the T1 affect the freesurfer segmentation in a way that we can't compare 1x1x1 with 0.8 x 0.8 x 0.8? Also, we would like to use T2s or FLAIRs as additional inputs to improve the results. Which sequence is preferably recommended? In our case, most controls and patients have the same FLAIR sequence, so to keep it consistent we would probably use FLAIR if that's worth it. Finally, we also have different T2s: some isotropic, some anisotropic and partial cooverage of the brain, and some anisotropic that are aligned to the hippocampus (resolution: 1x1x3, best resolution on coronal slices). Considering that they are just additional inputs, do they have to be consistent as well? In other words, should we *only* compare patients and controls that had the same T2 sequence as additional input and same T1 sequence as main input, or can we "mix and match" the additional inputs? Thank you in advance for your help, Renata ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Fs 6.0 dev version update
Hi Douglas, Thank you for the quick response. Maybe I didn't explain it well enough, I am downloading it from here: ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/dev/ I know it is the developmental version, but we are looking at the subregions and that's the only way we can. My question was about the change between the different developmental versions 11.08.16 and 14.08.16, I was wondering if whatever had been changed between them would affect the Hippocampus Subfields. Thanks! Renata On Wed, Aug 24, 2016 at 5:28 PM, Douglas Greve <gr...@nmr.mgh.harvard.edu> wrote: > Hi Renata, version 6 is not ready and should not be used. As far as we > know, there is not a link to 6.0 anywhere on our web pages. Where did you > find it? > > doug > > On 8/24/16 5:48 AM, Vaz pandolfo, Renata wrote: > > Dear FS experts, > > I downloaded the FS 6.0 dev version for Linux on 11.08.2016 and now I see > that there is a new version since the 14th of August. > > I ran about 20 recon-alls with the 11.08 version and now I am wondering if > there were any major changes between that and the new one, and if so, > whether I should rerun anything. > > I am assuming that having the newest version is always better, but I would > rather check if it is necessary before downloading the new one and > rerunning all the recon-alls. > > > Thanks! > > Renata > > Ps.: I am using the hippocampal subfields flag and checking the volumes of > the subregions of the hippocampus. > > > ___ > Freesurfer mailing > listfreesur...@nmr.mgh.harvard.eduhttps://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 > > > The information in this e-mail is intended only for the person to whom it > is > addressed. If you believe this e-mail was sent to you in error and the > e-mail > contains patient information, please contact the Partners Compliance > HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. > > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] output description
Dear FS experts, Is there a complete list of all output files followed by their description? The one I can find online seems to be incomplete (and/or out of date): https://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllOutputFiles#A-allOutputFiles For example, the volumes brain.mgz and brainmask.mgz.If I would like to quickly check what the difference between them is, where should I look? Thank you! Renata ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] Fs 6.0 dev version update
Dear FS experts, I downloaded the FS 6.0 dev version for Linux on 11.08.2016 and now I see that there is a new version since the 14th of August. I ran about 20 recon-alls with the 11.08 version and now I am wondering if there were any major changes between that and the new one, and if so, whether I should rerun anything. I am assuming that having the newest version is always better, but I would rather check if it is necessary before downloading the new one and rerunning all the recon-alls. Thanks! Renata Ps.: I am using the hippocampal subfields flag and checking the volumes of the subregions of the hippocampus. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] recon-all exited with error: reading lh.BA1_exvivo.label
Okay, I changed some other things and now the recon-all is running. I will see how it looks tomorrow. I used: recon-all -all \ > -i ~/Documents/Daten_Renata/Hippocampus_data/T1s_and_T2s/20110815/co_T1_20110815.nii.gz -s new_trial_20110815 \ > -sd ~/Documents/Daten_Renata/Hippocampus_data/T1s_and_T2s/20110815/ \ > -T2 ~/Documents/Daten_Renata/Hippocampus_data/T1s_and_T2s/20110815/o20160524_143200t2tirmcordarkfluidhipp3mmGRAPPAs006a1001.nii.gz \ > -T2pial -hippocampal-subfields-T1 Thanks! On Thu, Jul 7, 2016 at 2:15 PM, Vaz pandolfo, Renata <r...@njit.edu> wrote: > Thank you! > > But now the error is: > > ERROR: cannot find > o20160524_143200t2tirmcordarkfluidhipp3mmGRAPPAs006a1001.nii.gz > Linux lundb2 4.4.0-24-generic #43-Ubuntu SMP Wed Jun 8 19:27:37 UTC 2016 > x86_64 x86_64 x86_64 GNU/Linux > > recon-all -s 20110815 exited with ERRORS at Do 7. Jul 14:14:09 CEST 2016 > > Maybe I have to put the whole path? > > On Thu, Jul 7, 2016 at 2:10 PM, Krieger, Donald N. <krieg...@upmc.edu> > wrote: > >> Hi Renata, >> >> >> >> Is there a problem with the “-s” argument, i.e. the “/” in - s 20110815/ >> >> >> >> HTH - Don >> >> >> >> *From:* freesurfer-boun...@nmr.mgh.harvard.edu [mailto: >> freesurfer-boun...@nmr.mgh.harvard.edu] *On Behalf Of *Vaz pandolfo, >> Renata >> *Sent:* Thursday, July 07, 2016 8:05 AM >> *To:* freesurfer@nmr.mgh.harvard.edu >> *Subject:* [Freesurfer] recon-all exited with error: reading >> lh.BA1_exvivo.label >> >> >> >> Dear FreeSurfer developers, >> >> I am running recon-all on a healthy subject and I am also trying to get >> the hippocampal subfields segmentation. >> On the mri directory there is no hippocampus output, and the recon-all >> exited with errors. >> From my understanding, the error is with the lh.BA1_exvivo.label: >> >> SUBJECTS_DIR >> /home/lub_jungs/Documents/Daten_Renata/Hippocampus_data/T1s_and_T2s/20110815 >> FREESURFER_HOME /usr/local/freesurfer >> Loading source label. >> Invalid argument >> ERROR reading >> /home/lub_jungs/Documents/Daten_Renata/Hippocampus_data/T1s_and_T2s/20110815/fsaverage/label/lh.BA1_exvivo.label >> >> The command I used was: >> recon-all -all \ >> -i >> ~/Documents/Daten_Renata/Hippocampus_data/T1s_and_T2s/20110815/co_T1_20110815.nii.gz >> -s 20110815/ \ >> -sd ~/Documents/Daten_Renata/Hippocampus_data/T1s_and_T2s/20110815/ \ >> -T2 o20160524_143200t2tirmcordarkfluidhipp3mmGRAPPAs006a1001.nii.gz \ >> -T2pial -hippocampal-subfields-T1 >> >> >> When trying to solve the problem, I noticed that I could have run a >> separate command for the hippocampal subfields and I ran this one: >> >> >> recon-all \ >> -s 20110815/ \ >> -sd ~/Documents/Daten_Renata/Hippocampus_data/T1s_and_T2s/20110815/ \ >> -hippocampal-subfields-T1T2 >> ~/Documents/Daten_Renata/Hippocampus_data/T1s_and_T2s/20110815/o20160524_143200t2tirmcordarkfluidhipp3mmGRAPPAs006a1001.nii.gz >> 20110815_T2 >> >> Since the previous data had errors, I didn't really expect this to work, >> but I tried it anyways. >> >> It exited "without errors", but on the log there was the following error >> twice: >> >> Error:Cannot find CTF archive >> /usr/local/freesurfer/bin/segmentSubjectT1T2_autoEstimateAlveusML.ctf >> >> Extra info: >> >> Freesurfer version: freesurfer-Linux-centos6_x86_64-dev-20160616-8264611 >> >> uname -a: Linux lundb2 4.4.0-24-generic #43-Ubuntu SMP Wed Jun 8 19:27:37 >> UTC 2016 x86_64 x86_64 x86_64 GNU/Linux >> >> logs: recon-all and hippocampal-subfields-T1T2 attached >> >> If anyone has had the same problem, could you please tell me how to solve >> it? >> And if I am doing something wrong, please tell me the correct way so I >> can continue with the analysis. >> >> >> >> Thank you! >> >> Renata >> >> ___ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> The information in this e-mail is intended only for the person to whom it >> is >> addressed. If you believe this e-mail was sent to you in error and the >> e-mail >> contains patient information, please contact the Partners Compliance >> HelpLine at >> http://www.partners.org/complianceline . If the e-mail was sent to you >> in error >> but does not contain patient information, please contact the sender and >> properly >> dispose of the e-mail. >> >> > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] recon-all exited with error: reading lh.BA1_exvivo.label
Thank you! But now the error is: ERROR: cannot find o20160524_143200t2tirmcordarkfluidhipp3mmGRAPPAs006a1001.nii.gz Linux lundb2 4.4.0-24-generic #43-Ubuntu SMP Wed Jun 8 19:27:37 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux recon-all -s 20110815 exited with ERRORS at Do 7. Jul 14:14:09 CEST 2016 Maybe I have to put the whole path? On Thu, Jul 7, 2016 at 2:10 PM, Krieger, Donald N. <krieg...@upmc.edu> wrote: > Hi Renata, > > > > Is there a problem with the “-s” argument, i.e. the “/” in - s 20110815/ > > > > HTH - Don > > > > *From:* freesurfer-boun...@nmr.mgh.harvard.edu [mailto: > freesurfer-boun...@nmr.mgh.harvard.edu] *On Behalf Of *Vaz pandolfo, > Renata > *Sent:* Thursday, July 07, 2016 8:05 AM > *To:* freesurfer@nmr.mgh.harvard.edu > *Subject:* [Freesurfer] recon-all exited with error: reading > lh.BA1_exvivo.label > > > > Dear FreeSurfer developers, > > I am running recon-all on a healthy subject and I am also trying to get > the hippocampal subfields segmentation. > On the mri directory there is no hippocampus output, and the recon-all > exited with errors. > From my understanding, the error is with the lh.BA1_exvivo.label: > > SUBJECTS_DIR > /home/lub_jungs/Documents/Daten_Renata/Hippocampus_data/T1s_and_T2s/20110815 > FREESURFER_HOME /usr/local/freesurfer > Loading source label. > Invalid argument > ERROR reading > /home/lub_jungs/Documents/Daten_Renata/Hippocampus_data/T1s_and_T2s/20110815/fsaverage/label/lh.BA1_exvivo.label > > The command I used was: > recon-all -all \ > -i > ~/Documents/Daten_Renata/Hippocampus_data/T1s_and_T2s/20110815/co_T1_20110815.nii.gz > -s 20110815/ \ > -sd ~/Documents/Daten_Renata/Hippocampus_data/T1s_and_T2s/20110815/ \ > -T2 o20160524_143200t2tirmcordarkfluidhipp3mmGRAPPAs006a1001.nii.gz \ > -T2pial -hippocampal-subfields-T1 > > > When trying to solve the problem, I noticed that I could have run a > separate command for the hippocampal subfields and I ran this one: > > > recon-all \ > -s 20110815/ \ > -sd ~/Documents/Daten_Renata/Hippocampus_data/T1s_and_T2s/20110815/ \ > -hippocampal-subfields-T1T2 > ~/Documents/Daten_Renata/Hippocampus_data/T1s_and_T2s/20110815/o20160524_143200t2tirmcordarkfluidhipp3mmGRAPPAs006a1001.nii.gz > 20110815_T2 > > Since the previous data had errors, I didn't really expect this to work, > but I tried it anyways. > > It exited "without errors", but on the log there was the following error > twice: > > Error:Cannot find CTF archive > /usr/local/freesurfer/bin/segmentSubjectT1T2_autoEstimateAlveusML.ctf > > Extra info: > > Freesurfer version: freesurfer-Linux-centos6_x86_64-dev-20160616-8264611 > > uname -a: Linux lundb2 4.4.0-24-generic #43-Ubuntu SMP Wed Jun 8 19:27:37 > UTC 2016 x86_64 x86_64 x86_64 GNU/Linux > > logs: recon-all and hippocampal-subfields-T1T2 attached > > If anyone has had the same problem, could you please tell me how to solve > it? > And if I am doing something wrong, please tell me the correct way so I can > continue with the analysis. > > > > Thank you! > > Renata > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > The information in this e-mail is intended only for the person to whom it > is > addressed. If you believe this e-mail was sent to you in error and the > e-mail > contains patient information, please contact the Partners Compliance > HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. > > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
