Re: [Freesurfer] Problem with freeview
Dear Ruopeng, I didn't install it myself, but I guess it is a stable one. Are you suggesting the timecourse option might simply not be available in the stable version? thanks fabio ___ 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] some questions about optseq
I don't understand what you are trying to do. Can you elaborate? There is no way to make optseq produce a sequence where two events always occur in a certain order On 6/20/14 4:27 AM, charujing123 wrote: Hi FS experts, I try to design the schedule by optseq2. However it is beyond my ability as our experiment has a little complicated. Here is our goal: two successive trials decide condition. For example, this is our sequence:2 2 1 1 2 2 2 1 1 2 2 1 2 1 1 2 1 2 2 1 1 1 1 2 2 2 2 1 1 1 2 1 2 1 1 1 1 1 1 2 1 2 1 2 1 2 1 2 2 1 1 2 2 2 2 2 2 1 1 1 2 2 2 1 2 2 2 2 1 2 2 1 1 2 1 1 2 1 1 1 2 .22 and 11 is the same condition(this condition has 40 repeats); 12 and 21 is the same condition(this condition also has 40 repeats). That is to say, there are two conditons in this run. 81 trials in this run, and each trial has 1.5s intervels. And mean intertrial intervals is 3.5s. Our TR is 2s. According the efficiency about these two conditions, how could I design the intertrial intervals to get a appropriate sequence? I tried this: optseq2 --ntp 203 --tr 2 --psdwin 0 20 --ev ev1 2 40 --ev ev2 2 40 --nkeep 2 --o ex2 --nsearch 1000 Although it echo a result, I know, it is not what I need, because of every condition having two trials. So how I complete that? Thanks. All the best. Rujing Zha 2014-06-20 charujing123 ___ 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 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] Can some send me rh.average.curvature.filled.buckner40.tif file
Dear All, when I run recon-all I encounter errro saying that rh.average.curvature.filled.buckner40.tif file is missing. I found this file missing in my average folder so if someone can send it as an attachment or guide me to where I can find it it will be great help. Many thanks in advance Venkat ___ 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] mpr2mni305 failed, see transforms/talairach_avi.log
Hi All, I am getting the the following error when I run recon-all -subjid E368 -autorecon1 ERROR: mpr2mni305 failed, see transforms/talairach_avi.log Here is what talairach_avi.log says /home/administrator/Desktop/freesurfer/subjects_dir/E368/mri /usr/local/freesurfer/bin/talairach_avi --i orig_nu.mgz --xfm transforms/talairach.auto.xfm $Id: talairach_avi,v 1.9 2011/03/02 18:38:06 nicks Exp $ Linux administrator-HP-Pro-3330-MT 3.13.0-24-generic #46-Ubuntu SMP Thu Apr 10 19:08:14 UTC 2014 i686 i686 i686 GNU/Linux Fri Jun 20 17:06:38 IST 2014 mri_convert orig_nu.mgz talsrcimg.img $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from orig_nu.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) writing to talsrcimg.img... Analyze Output Matrix -1.000 0.000 0.000 129.000; 0.000 0.000 1.000 -129.000; 0.000 -1.000 0.000 122.500; 0.000 0.000 0.000 1.000; INFO: set hdr.hist.orient to -1 mpr2mni305 talsrcimg Fri Jun 20 17:06:39 IST 2014 /usr/local/freesurfer/bin/mpr2mni305 talsrcimg $Id: mpr2mni305,v 1.4 2009/06/03 16:01:38 nicks Exp $ target=711-2C_as_mni_average_305 - analyzeto4dfp talsrcimg -O0 -y - $Id: ifh2hdr.c,v 1.3 2007/05/05 10:45:03 nicks Exp $ Fri Jun 20 17:06:40 2014 Writing: talsrcimg.4dfp.hdr $Id: analyzeto4dfp.c,v 1.2 2007/05/05 00:00:06 nicks Exp $ Reading: talsrcimg.hdr header size 348 bytes hdr.dime.datatypeoffset=70value=2 hdr.dime.bitpixoffset=72value=8 hdr.hist.orientoffset=252value=-1 dimensionality 4 dimensions 256 256 256 1 Reading: talsrcimg.img Writing: talsrcimg.4dfp.img Writing: talsrcimg.4dfp.ifh ifh2hdr talsrcimg -r0to255 ori=2 - gauss_4dfp talsrcimg 1.1 - $Id: gauss_4dfp.c,v 1.3 2009/05/15 21:43:46 nicks Exp $ Reading: talsrcimg.4dfp.img Writing: talsrcimg_g11.4dfp.img image dimensions 256 256 256 padded to 288 288 288 processing volume 1$Id: ifh2hdr.c,v 1.3 2007/05/05 10:45:03 nicks Exp $ Fri Jun 20 17:06:46 2014 Writing: talsrcimg_g11.4dfp.hdr Writing: talsrcimg_g11.4dfp.ifh including: talsrcimg.4dfp.img.rec in talsrcimg_g11.4dfp.img.rec - imgreg_4dfp /usr/local/freesurfer/average/711-2C_as_mni_average_305 none talsrcimg_g11 none talsrcimg_to_711-2C_as_mni_average_305_t4 4355 - $Id: imgreg_4dfp.c,v 1.4 2010/02/27 01:41:53 nicks Exp $ imgreg_4dfp: /usr/local/freesurfer/average/711-2C_as_mni_average_305.4dfp.img read error /usr/local/freesurfer/average/711-2C_as_mni_average_305.4dfp.img 256 256 256 1 1.00 1.00 1.00 orientation T byte_order littleendian Reading image: /usr/local/freesurfer/average/711-2C_as_mni_average_305.4dfp.img dimensions: 256 256 256 mmppix: 1. -1. -1. center: 128. -129. -129. ERROR: 'imgreg_4dfp /usr/local/freesurfer/average/711-2C_as_mni_average_305 none talsrcimg_g11 none talsrcimg_to_711-2C_as_mni_average_305_t4 4355' failed! status=255 ERROR: mpr2mni305 execution aborted Any help will be greatly appreciated. Thanks Venkat ___ 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] some questions about optseq
Hi doug, Thanks doug. In our experiment, there are 324s, and TR=2s, two kinds of stimulus. Each one consisted of 3 components(cue 500ms + fixation 500ms + picture 500ms), and will be presented with a interval of 1.5s. After stimulus onset, followed by reaction time. One stimulus will repeat 41 times, the other 40 times. Based on optseq2 --ntp 162 --tr 2 --psdwin 0 20 --ev ev1 2 40 --ev ev2 2 40 --nkeep 2 --o ex2 --nsearch 1000, how should I modify to get a efficient sequence, as I have no idea about NULL design. Thanks again All the best Rujing Zha 2014-06-20 charujing123 发件人：Douglas Greve gr...@nmr.mgh.harvard.edu 发送时间：2014-06-20 16:51 主题：Re: [Freesurfer] some questions about optseq 收件人：freesurferfreesurfer@nmr.mgh.harvard.edu 抄送： I don't understand what you are trying to do. Can you elaborate? There is no way to make optseq produce a sequence where two events always occur in a certain order On 6/20/14 4:27 AM, charujing123 wrote: Hi FS experts, I try to design the schedule by optseq2. However it is beyond my ability as our experiment has a little complicated. Here is our goal: two successive trials decide condition. For example, this is our sequence:2 2 1 1 2 2 2 1 1 2 2 1 2 1 1 2 1 2 2 1 1 1 1 2 2 2 2 1 1 1 2 1 2 1 1 1 1 1 1 2 1 2 1 2 1 2 1 2 2 1 1 2 2 2 2 2 2 1 1 1 2 2 2 1 2 2 2 2 1 2 2 1 1 2 1 1 2 1 1 1 2 .22 and 11 is the same condition(this condition has 40 repeats); 12 and 21 is the same condition(this condition also has 40 repeats). That is to say, there are two conditons in this run. 81 trials in this run, and each trial has 1.5s intervels. And mean intertrial intervals is 3.5s. Our TR is 2s. According the efficiency about these two conditions, how could I design the intertrial intervals to get a appropriate sequence? I tried this: optseq2 --ntp 203 --tr 2 --psdwin 0 20 --ev ev1 2 40 --ev ev2 2 40 --nkeep 2 --o ex2 --nsearch 1000 Although it echo a result, I know, it is not what I need, because of every condition having two trials. So how I complete that? Thanks. All the best. Rujing Zha 2014-06-20 charujing123 ___ 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 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] some questions about optseq
I don't think there is anything wrong with what you have. Is there a problem? You could shorten it to something like 240sec or so. On 6/20/14 1:43 PM, charujing123 wrote: Hi doug, Th?anks doug. In our experiment, there are 324s, and TR=2s, two kinds of stimulus. Each one consisted of 3 components(cue 500ms + fixation 500ms + picture 500ms), and will be presented with a interval of 1.5s. After stimulus onset, followed by reaction time. One stimulus will repeat 41 times, the other 40 times. Based on optseq2 --ntp 162 --tr 2 --psdwin 0 20 --ev ev1 2 40 --ev ev2 2 40 --nkeep 2 --o ex2 --nsearch 1000, how should I modify to get a efficient sequence, as I have no idea about NULL design. Thanks again All the best Rujing Zha 2014-06-20 charujing123 *? ??:*Douglas Greve gr...@nmr.mgh.harvard.edu *? ???:*2014-06-20 16:51 *? ?:*Re: [Freesurfer] some questions about optseq *? ??:*freesurferfreesurfer@nmr.mgh.harvard.edu *? ?:* I don't understand what you are trying to do. Can you elaborate? There is no way to make optseq produce a sequence where two events always occur in a certain order On 6/20/14 4:27 AM, charujing123 wrote: Hi FS experts, I try to design the schedule by optseq2. However it is beyond my ability as our experiment has a little complicated. Here is our goal: two successive trials decide condition. For example, this is our sequence:2 2 1 1 2 2 2 1 1 2 2 1 2 1 1 2 1 2 2 1 1 1 1 2 2 2 2 1 1 1 2 1 2 1 1 1 1 1 1 2 1 2 1 2 1 2 1 2 2 1 1 2 2 2 2 2 2 1 1 1 2 2 2 1 2 2 2 2 1 2 2 1 1 2 1 1 2 1 1 1 2 .22 and 11 is the same condition(this condition has 40 repeats); 12 and 21 is the same condition(this condition also has 40 repeats). That is to say, there are two conditons in this run. 81 trials in this run, and each trial has 1.5s intervels. And mean intertrial intervals is 3.5s. Our TR is 2s. According the efficiency about these two conditions, how could I design the intertrial intervals to get a appropriate sequence? I tried this: optseq2 --ntp 203 --tr 2 --psdwin 0 20 --ev ev1 2 40 --ev ev2 2 40 --nkeep 2 --o ex2 --nsearch 1000 Although it echo a result, I know, it is not what I need, because of every condition having two trials. So how I complete that? Thanks. All the best. Rujing Zha 2014-06-20 charujing123 ___ 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 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] Problem with freeview
That is correct. timecourse option is only available in dev version. You can download it here: https://surfer.nmr.mgh.harvard.edu/fswiki/Download You may want to make a backup of your current freeview.bin file. Ruopeng On Jun 20, 2014, at 3:25 AM, Bernardoni, Fabio fabio.bernard...@uniklinikum-dresden.de wrote: Dear Ruopeng, I didn't install it myself, but I guess it is a stable one. Are you suggesting the timecourse option might simply not be available in the stable version? thanks fabio ___ 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 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] problem of Label file
Dear Bruce No, I used QDEC to create label. It should be fsaverage. Wang Kangcheng Faculty of Psychology, Southwest University, China Email: kangchengwang0...@gmail.com / wangkangcheng@163.com Address: No.2 Tiansheng Road, BeiBei District, Chongqing, 400715,P.R.China 在 2014年6月19日，下午10:00，Bruce Fischl fis...@nmr.mgh.harvard.edu 写道： using tksurfer? On what fsaverage? On Thu, 19 Jun 2014, wangkangcheng_gmail wrote: Dear Bruce, I creat the file of label according to the manual of free surfer. The websitewas http://www.freesurfer.net/fswiki/FsTutorial/QdecGroupAnalysis_freeview. (1) hold down shift then left click and drag to draw the ROI. (2) save the label by selecting File -- Save Label. Thank you very much. Wang Kangcheng Faculty of Psychology, Southwest University, China Email: kangchengwang0...@gmail.com / wangkangcheng@163.com Address: No.2 Tiansheng Road, BeiBei District, Chongqing, 400715,P.R.China 在 2014年6月19日，下午9:45，Bruce Fischl fis...@nmr.mgh.harvard.edu 写道： hmmm, the sig.mgh looks fine. No outlier values in it. Can you give us a detailed description of how you created the label? This seems like a bug. cheers Bruce On Thu, 19 Jun 2014, wangkangcheng_gmail wrote: I’m sorry. I am a new learner of freesurfer and don’t know whether the numbers are reasonable. The sig.mgh and file of label was in the attachment. Thank you. 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
Re: [Freesurfer] Labels to annotation
We do not have a way to resolve the overlapping problem. That is something you will have to figure out. You should be able to keep the colors the same by specifying the entries in the color table doug On 6/19/14 3:41 PM, Karen Marie Sandø Ambrosen wrote: Dear Freesurfer experts, I have made a parcellation of the white matter surface outside of freesurfer in volumes. I convert the volume labels to surface labels. I have now a lot of surface labels (~500 for each hemisphere) which I want to concatenate to an annotation file for easier visualization. When I use mris_label2annot to perform this operation I get a lot of warnings: WARNING: vertex 6021 maps to multiple labels! (overwriting), and the result does not look right. When I load some of the single labels into freeview or tksurfer they look fine. Does anyone know how to perform this operation? How do I avoid the warnings? I do the operations (volume labels--surface labels--annotation) on each hemisphere separately, but I have some regions located in both hemispheres. Is it then possible to keep the whole region the same color across hemispheres during the operations? Best, Karen ___ 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 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] FLASH and MPRAGE sequences for segmentation on a GE 3.0T
Freesurfer, We recently gained access to a new GE Discovery MR750w 3.0T GEM MRI with a 24 channel headcoil. Because this system is located at a nearby hospital and is used clinically, we do not have a research agreement with GE in place and, therefore, cannot edit the default pulse sequences. We were wondering what scans/parameters would give us optimal segmentation (similar to MPRAGE and/or FLASH at https://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferWiki?action=AttachFiledo=gettarget=FreeSurfer_Suggested_Morphometry_Protocols.pdf). Thanks, Matthew Sherwood Medical Research Engineer Wright State Research Institute 4035 Colonel Glenn Hwy. Dayton, OH 45431 PH: 937.705.1025 FAX: 937.705.1095 EMAIL: matt.sherw...@wright.edumailto:matt.sherw...@wright.edu ___ 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] some questions about optseq
On 6/20/14 4:14 PM, charujing123 wrote: Hi doug, Thanks doug. Here are two questions that I am not sure: 1, Each stimulus condition has three elements, i.e. cue fixation and picture. However it is only picture element that will be analyzed. The time window of picture will not influence the efficiency of sequence? Not much 2, After stimulus presented(last 1.5s), subjects will response to the picture in the specific time window. This time window followed the stimulus, and it varied from 2.5s to ~8.5s. However, some trials was not followed by NULL trial. That is to say, there is no time to response after some trials. You can create a minimum fixed amount of after the trial with --tnullmin doug Thanks All the best Rujing Zha 2014-06-20 charujing123 *? ??:*Douglas Greve gr...@nmr.mgh.harvard.edu *? ???:*2014-06-20 21:18 *? ?:*Re: [Freesurfer] some questions about optseq *? ??:*freesurferfreesurfer@nmr.mgh.harvard.edu *? ?:* I don't think there is anything wrong with what you have. Is there a problem? You could shorten it to something like 240sec or so. On 6/20/14 1:43 PM, charujing123 wrote: Hi doug, Th?anks doug. In our experiment, there are 324s, and TR=2s, two kinds of stimulus. Each one consisted of 3 components(cue 500ms + fixation 500ms + picture 500ms), and will be presented with a interval of 1.5s. After stimulus onset, followed by reaction time. One stimulus will repeat 41 times, the other 40 times. Based on optseq2 --ntp 162 --tr 2 --psdwin 0 20 --ev ev1 2 40 --ev ev2 2 40 --nkeep 2 --o ex2 --nsearch 1000, how should I modify to get a efficient sequence, as I have no idea about NULL design. Thanks again All the best Rujing Zha 2014-06-20 charujing123 *? ??:*Douglas Greve gr...@nmr.mgh.harvard.edu *? ???:*2014-06-20 16:51 *? ?:*Re: [Freesurfer] some questions about optseq *? ??:*freesurferfreesurfer@nmr.mgh.harvard.edu *? ?:* I don't understand what you are trying to do. Can you elaborate? There is no way to make optseq produce a sequence where two events always occur in a certain order On 6/20/14 4:27 AM, charujing123 wrote: Hi FS experts, I try to design the schedule by optseq2. However it is beyond my ability as our experiment has a little complicated. Here is our goal: two successive trials decide condition. For example, this is our sequence:2 2 1 1 2 2 2 1 1 2 2 1 2 1 1 2 1 2 2 1 1 1 1 2 2 2 2 1 1 1 2 1 2 1 1 1 1 1 1 2 1 2 1 2 1 2 1 2 2 1 1 2 2 2 2 2 2 1 1 1 2 2 2 1 2 2 2 2 1 2 2 1 1 2 1 1 2 1 1 1 2 .22 and 11 is the same condition(this condition has 40 repeats); 12 and 21 is the same condition(this condition also has 40 repeats). That is to say, there are two conditons in this run. 81 trials in this run, and each trial has 1.5s intervels. And mean intertrial intervals is 3.5s. Our TR is 2s. According the efficiency about these two conditions, how could I design the intertrial intervals to get a appropriate sequence? I tried this: optseq2 --ntp 203 --tr 2 --psdwin 0 20 --ev ev1 2 40 --ev ev2 2 40 --nkeep 2 --o ex2 --nsearch 1000 Although it echo a result, I know, it is not what I need, because of every condition having two trials. So how I complete that? Thanks. All the best. Rujing Zha 2014-06-20 charujing123 ___ 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 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] some questions about optseq
Hi doug, Thanks doug. Here are two questions that I am not sure: 1, Each stimulus condition has three elements, i.e. cue fixation and picture. However it is only picture element that will be analyzed. The time window of picture will not influence the efficiency of sequence? 2, After stimulus presented(last 1.5s), subjects will response to the picture in the specific time window. This time window followed the stimulus, and it varied from 2.5s to ~8.5s. However, some trials was not followed by NULL trial. That is to say, there is no time to response after some trials. Thanks All the best Rujing Zha 2014-06-20 charujing123 发件人：Douglas Greve gr...@nmr.mgh.harvard.edu 发送时间：2014-06-20 21:18 主题：Re: [Freesurfer] some questions about optseq 收件人：freesurferfreesurfer@nmr.mgh.harvard.edu 抄送： I don't think there is anything wrong with what you have. Is there a problem? You could shorten it to something like 240sec or so. On 6/20/14 1:43 PM, charujing123 wrote: Hi doug, Thanks doug. In our experiment, there are 324s, and TR=2s, two kinds of stimulus. Each one consisted of 3 components(cue 500ms + fixation 500ms + picture 500ms), and will be presented with a interval of 1.5s. After stimulus onset, followed by reaction time. One stimulus will repeat 41 times, the other 40 times. Based on optseq2 --ntp 162 --tr 2 --psdwin 0 20 --ev ev1 2 40 --ev ev2 2 40 --nkeep 2 --o ex2 --nsearch 1000, how should I modify to get a efficient sequence, as I have no idea about NULL design. Thanks again All the best Rujing Zha 2014-06-20 charujing123 发 件人：Douglas Greve gr...@nmr.mgh.harvard.edu 发 送时间：2014-06-20 16:51 主 题：Re: [Freesurfer] some questions about optseq 收 件人：freesurferfreesurfer@nmr.mgh.harvard.edu 抄 送： I don't understand what you are trying to do. Can you elaborate? There is no way to make optseq produce a sequence where two events always occur in a certain order On 6/20/14 4:27 AM, charujing123 wrote: Hi FS experts, I try to design the schedule by optseq2. However it is beyond my ability as our experiment has a little complicated. Here is our goal: two successive trials decide condition. For example, this is our sequence:2 2 1 1 2 2 2 1 1 2 2 1 2 1 1 2 1 2 2 1 1 1 1 2 2 2 2 1 1 1 2 1 2 1 1 1 1 1 1 2 1 2 1 2 1 2 1 2 2 1 1 2 2 2 2 2 2 1 1 1 2 2 2 1 2 2 2 2 1 2 2 1 1 2 1 1 2 1 1 1 2 .22 and 11 is the same condition(this condition has 40 repeats); 12 and 21 is the same condition(this condition also has 40 repeats). That is to say, there are two conditons in this run. 81 trials in this run, and each trial has 1.5s intervels. And mean intertrial intervals is 3.5s. Our TR is 2s. According the efficiency about these two conditions, how could I design the intertrial intervals to get a appropriate sequence? I tried this: optseq2 --ntp 203 --tr 2 --psdwin 0 20 --ev ev1 2 40 --ev ev2 2 40 --nkeep 2 --o ex2 --nsearch 1000 Although it echo a result, I know, it is not what I need, because of every condition having two trials. So how I complete that? Thanks. All the best. Rujing Zha 2014-06-20 charujing123 ___ 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 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] mri_label2label results
yes, that's a lovely idea, but it is very, very difficult to get NIH funding to support such a thing. cheers Bruce On Fri, 20 Jun 2014, Yang, Daniel wrote: That is great to know! I personally feel that there should be some sort of autoupdate function or patch file list in FreeSurfer so that when a bug like this is fixed, FreeSurfer can be updated automatically or we can apply the patch from the website. I think the one currently released should be FreeSurfer 5.3.1, with this bug fixed. This bug could have invalidated the research results to some extent if one is retrieving ROI-based stats manually, I feel. Many major software tend to have bugs after release, like SPSS, so this should be a routine... These are just my two cents. Daniel On Jun 19, 2014, at 10:20 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Yes, it was only mri_label2label has that bug On Jun 19, 2014, at 10:14 PM, Yang, Daniel yung-jui.y...@yale.edu wrote: Thanks! Is there a list of bug fixed (after release) somewhere? Should we use the development version instead? Please tell me that it is only mri_label2label that has a bug … On 6/19/14, 9:08 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: I think it was a bug we fixed after the release. We can send you new versions on those operating systems and you can try them out. Zeke: can you get Daniel new versions of mri_label2label? thanks Bruce On Fri, 20 Jun 2014, Yang, Daniel wrote: Ah, it¹s FreeSurfer 5.3 ‹ Release Date 15 May 2013. Do you mean that the FreeSurfer 5.3 was updated after 05/15/2013? Thanks, Daniel On 6/19/14, 7:55 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: what version are you using? I think this is a bug we fixed a few months ago. Or another one Bruce On Thu, 19 Jun 2014, Yang, Daniel wrote: Dear all, I found that mri_label2label generates different results, depending on whether the software¹s platform is MacOS Lion or CentOS 6. Is this possible? Thanks! Daniel ___ 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 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] some questions about optseq
weird? I'll need something more specific than that On 6/20/14 4:57 PM, charujing123 wrote: Hi doug Thanks very much. I see. When I add --tnullmin 2 --tnullmax 8, result looks weird. === [psylab16@centos1 ~]$ cat ex1-001.par 0.22.000 1. ev2 2.02.000 1. NULL 4.12.000 1. ev1 6.02.000 1. NULL 8.12.000 1. ev1 10.02.000 1. NULL 12.12.000 1. ev1 14.02.000 1. NULL 16.12.000 1. ev1 18.02.000 1. NULL 20.22.000 1. ev2 22.02.000 1. NULL 24.12.000 1. ev1 26.02.000 1. NULL 28.12.000 1. ev1 30.02.000 1. NULL 32.22.000 1. ev2 34.02.000 1. NULL 36.22.000 1. ev2 38.02.000 1. NULL 40.22.000 1. ev2 42.02.000 1. NULL 44.22.000 1. ev2 46.02.000 1. NULL 48.12.000 1. ev1 50.02.000 1. NULL 52.22.000 1. ev2 54.02.000 1. NULL 56.12.000 1. ev1 58.02.000 1. NULL 60.22.000 1. ev2 62.02.000 1. NULL 64.22.000 1. ev2 66.02.000 1. NULL 68.12.000 1. ev1 70.02.000 1. NULL 72.12.000 1. ev1 74.02.000 1. NULL 76.12.000 1. ev1 78.02.000 1. NULL 80.22.000 1. ev2 82.02.000 1. NULL 84.22.000 1. ev2 86.02.000 1. NULL 88.22.000 1. ev2 90.02.000 1. NULL 92.12.000 1. ev1 94.02.000 1. NULL 96.12.000 1. ev1 98.02.000 1. NULL 100.12.000 1. ev1 102.02.000 1. NULL 104.22.000 1. ev2 106.02.000 1. NULL 108.12.000 1. ev1 110.02.000 1. NULL 112.12.000 1. ev1 114.02.000 1. NULL 116.22.000 1. ev2 118.02.000 1. NULL 120.12.000 1. ev1 122.02.000 1. NULL 124.22.000 1. ev2 126.02.000 1. NULL 128.22.000 1. ev2 130.02.000 1. NULL 132.22.000 1. ev2 134.02.000 1. NULL 136.12.000 1. ev1 138.02.000 1. NULL 140.22.000 1. ev2 142.02.000 1. NULL 144.22.000 1. ev2 146.02.000 1. NULL 148.22.000 1. ev2 150.02.000 1. NULL 152.22.000 1. ev2 154.02.000 1. NULL 156.12.000 1. ev1 158.02.000 1. NULL 160.22.000 1. ev2 162.02.000 1. NULL 164.22.000 1. ev2 166.02.000 1. NULL 168.12.000 1. ev1 170.02.000 1. NULL 172.22.000 1. ev2 174.02.000 1. NULL 176.12.000 1. ev1 178.02.000 1. NULL 180.22.000 1. ev2 182.02.000 1. NULL 184.22.000 1. ev2 186.02.000 1. NULL 188.12.000 1. ev1 190.02.000 1. NULL 192.12.000 1. ev1 194.02.000 1. NULL 196.12.000 1. ev1 198.02.000 1. NULL 200.12.000 1. ev1 202.02.000 1. NULL 204.22.000 1.
Re: [Freesurfer] Retinotopic mapping using selxavg3-sess
[sorry, I may have sent this multiple times, but, because I'm not sure if it got through because I got several bounce-back error messages, I'm sending it out again...] Thanks, Doug. I think I've kind of sorted that one out by creating a folder called Retinotopy under freesurfer/subjects/Retinotopy/3/, which contains the 001/, ... 004/ folders containing those their corresponding (polar and eccen) rtopy.par and f.nii files. But now I have another problem. When I run selxavg3-sess -a Retintopy.3.lh -s 3 , it runs up to the point as below, where it's using FSL's BET to Extract Brain. # -- Using FSL's BET to Extract Brain-- # /usr/local/freesurfer/subjects/Retinotopy/3/Retinotopy bet.fsl /tmp/mkbrainmask_9112/in.nii /tmp/mkbrainmask_9112/brain -m -f 0.1 /usr/local/freesurfer//bin/bet.fsl: 1: /usr/local/freesurfer//bin/bet.fsl: /bin/remove_ext: not found /usr/local/freesurfer//bin/bet.fsl: 1: /usr/local/freesurfer//bin/bet.fsl: /bin/remove_ext: not found /usr/local/freesurfer//bin/bet.fsl: 1: /usr/local/freesurfer//bin/bet.fsl: /bin/imtest: not found /usr/local/freesurfer//bin/bet.fsl: 153: [: =: unexpected operator /usr/local/freesurfer//bin/bet.fsl: 231: /usr/local/freesurfer//bin/bet.fsl: /bin/bet2: not found Then I realized that the program looks for those not-found files (remove_ext, imtest, bet2) in /bin/, but actually they're all in /usr/lib/fsl/5.0/. What I did next was to copy those files from /usr/lib/fsl/5.0/ to /bin/, but then I got this error: # -- Using FSL's BET to Extract Brain-- # /usr/local/freesurfer/subjects/Retinotopy/3/Retinotopy bet.fsl /tmp/mkbrainmask_12619/in.nii /tmp/mkbrainmask_12619/brain -m -f 0.1 /bin/bet2: error while loading shared libraries: libfslvtkio.so: cannot open shared object file: No such file or directory mri_binarize --i /tmp/mkbrainmask_12619/brain_mask.nii --min .01 --o /tmp/mkbrainmask_12619/brain_mask.nii niiRead(): error opening file /tmp/mkbrainmask_12619/brain_mask.nii Again, I tried copying the file libfslvtkio.so from /usr/lib/fsl/5.0 to /bin/, but it keeps giving me the same error. So I have two questions: 1) I suspect that selxavg3-sess should be looking for the files in /usr/lib/fsl/5.0 instead of in /bin/. Why does it do that? And how can I direct it to look for files in the former location instead? 2) As a quick fix, is it OK for me to copy all the files from /usr/lib/fsl/5.0 to /bin/? Will it solve the problem? The folder /bin/ contains something else and I don't really feel like messing with it. Many thanks, Alan -- Alan Lee sites.google.com/site/alanlflee/ On Thu, Jun 19, 2014 at 9:03 PM, Alan Lee alan@ens.fr wrote: Thanks, Doug. I think I've kind of sorted that one out by creating a folder called Retinotopy under freesurfer/subjects/Retinotopy/3/, which contains the 001/, ... 004/ folders containing those their corresponding (polar and eccen) rtopy.par and f.nii files. But now I have another problem. When I run selxavg3-sess -a Retintopy.3.lh -s 3 , it runs up to the point as below, where it's using FSL's BET to Extract Brain. # -- Using FSL's BET to Extract Brain-- # /usr/local/freesurfer/subjects/Retinotopy/3/Retinotopy bet.fsl /tmp/mkbrainmask_9112/in.nii /tmp/mkbrainmask_9112/brain -m -f 0.1 /usr/local/freesurfer//bin/bet.fsl: 1: /usr/local/freesurfer//bin/bet.fsl: /bin/remove_ext: not found /usr/local/freesurfer//bin/bet.fsl: 1: /usr/local/freesurfer//bin/bet.fsl: /bin/remove_ext: not found /usr/local/freesurfer//bin/bet.fsl: 1: /usr/local/freesurfer//bin/bet.fsl: /bin/imtest: not found /usr/local/freesurfer//bin/bet.fsl: 153: [: =: unexpected operator /usr/local/freesurfer//bin/bet.fsl: 231: /usr/local/freesurfer//bin/bet.fsl: /bin/bet2: not found Then I realized that the program looks for those not-found files (remove_ext, imtest, bet2) in /bin/, but actually they're all in /usr/lib/fsl/5.0/. What I did next was to copy those files from /usr/lib/fsl/5.0/ to /bin/, but then I got this error: # -- Using FSL's BET to Extract Brain-- # /usr/local/freesurfer/subjects/Retinotopy/3/Retinotopy bet.fsl /tmp/mkbrainmask_12619/in.nii /tmp/mkbrainmask_12619/brain -m -f 0.1 /bin/bet2: error while loading shared libraries: libfslvtkio.so: cannot open shared object file: No such file or directory mri_binarize --i /tmp/mkbrainmask_12619/brain_mask.nii --min .01 --o /tmp/mkbrainmask_12619/brain_mask.nii niiRead(): error opening file /tmp/mkbrainmask_12619/brain_mask.nii Again, I tried copying the file libfslvtkio.so from /usr/lib/fsl/5.0 to /bin/, but it keeps giving me the same error. So I have two questions: 1) I suspect that selxavg3-sess should be looking for the files in /usr/lib/fsl/5.0 instead of in /bin/. Why does it do that? And how can I direct it to look for files in the former location instead? 2) As a quick fix, is it OK for me to copy all
Re: [Freesurfer] Retinotopic mapping using selxavg3-sess
Sorry, I don't know why it is failing. We don't have a problem with it and no one else has reported this. Check the location of the FSLDIR env variable. Or maybe it is a new version of FSL that is not compatible with the old? On 6/20/14 5:25 PM, Alan Lee wrote: [sorry, I may have sent this multiple times, but, because I'm not sure if it got through because I got several bounce-back error messages, I'm sending it out again...] Thanks, Doug. I think I've kind of sorted that one out by creating a folder called Retinotopy under freesurfer/subjects/Retinotopy/3/, which contains the 001/, ... 004/ folders containing those their corresponding (polar and eccen) rtopy.par and f.nii files. But now I have another problem. When I run selxavg3-sess -a Retintopy.3.lh -s 3 , it runs up to the point as below, where it's using FSL's BET to Extract Brain. # -- Using FSL's BET to Extract Brain-- # /usr/local/freesurfer/subjects/Retinotopy/3/Retinotopy bet.fsl /tmp/mkbrainmask_9112/in.nii /tmp/mkbrainmask_9112/brain -m -f 0.1 /usr/local/freesurfer//bin/bet.fsl: 1: /usr/local/freesurfer//bin/bet.fsl: /bin/remove_ext: not found /usr/local/freesurfer//bin/bet.fsl: 1: /usr/local/freesurfer//bin/bet.fsl: /bin/remove_ext: not found /usr/local/freesurfer//bin/bet.fsl: 1: /usr/local/freesurfer//bin/bet.fsl: /bin/imtest: not found /usr/local/freesurfer//bin/bet.fsl: 153: [: =: unexpected operator /usr/local/freesurfer//bin/bet.fsl: 231: /usr/local/freesurfer//bin/bet.fsl: /bin/bet2: not found Then I realized that the program looks for those not-found files (remove_ext, imtest, bet2) in /bin/, but actually they're all in /usr/lib/fsl/5.0/. What I did next was to copy those files from /usr/lib/fsl/5.0/ to /bin/, but then I got this error: # -- Using FSL's BET to Extract Brain-- # /usr/local/freesurfer/subjects/Retinotopy/3/Retinotopy bet.fsl /tmp/mkbrainmask_12619/in.nii /tmp/mkbrainmask_12619/brain -m -f 0.1 /bin/bet2: error while loading shared libraries: libfslvtkio.so: cannot open shared object file: No such file or directory mri_binarize --i /tmp/mkbrainmask_12619/brain_mask.nii --min .01 --o /tmp/mkbrainmask_12619/brain_mask.nii niiRead(): error opening file /tmp/mkbrainmask_12619/brain_mask.nii Again, I tried copying the file libfslvtkio.so from /usr/lib/fsl/5.0 to /bin/, but it keeps giving me the same error. So I have two questions: 1) I suspect that selxavg3-sess should be looking for the files in /usr/lib/fsl/5.0 instead of in /bin/. Why does it do that? And how can I direct it to look for files in the former location instead? 2) As a quick fix, is it OK for me to copy all the files from /usr/lib/fsl/5.0 to /bin/? Will it solve the problem? The folder /bin/ contains something else and I don't really feel like messing with it. Many thanks, Alan -- Alan Lee sites.google.com/site/alanlflee/ http://sites.google.com/site/alanlflee/ On Thu, Jun 19, 2014 at 9:03 PM, Alan Lee alan@ens.fr mailto:alan@ens.fr wrote: Thanks, Doug. I think I've kind of sorted that one out by creating a folder called Retinotopy under freesurfer/subjects/Retinotopy/3/, which contains the 001/, ... 004/ folders containing those their corresponding (polar and eccen) rtopy.par and f.nii files. But now I have another problem. When I run selxavg3-sess -a Retintopy.3.lh -s 3 , it runs up to the point as below, where it's using FSL's BET to Extract Brain. # -- Using FSL's BET to Extract Brain-- # /usr/local/freesurfer/subjects/Retinotopy/3/Retinotopy bet.fsl /tmp/mkbrainmask_9112/in.nii /tmp/mkbrainmask_9112/brain -m -f 0.1 /usr/local/freesurfer//bin/bet.fsl: 1: /usr/local/freesurfer//bin/bet.fsl: /bin/remove_ext: not found /usr/local/freesurfer//bin/bet.fsl: 1: /usr/local/freesurfer//bin/bet.fsl: /bin/remove_ext: not found /usr/local/freesurfer//bin/bet.fsl: 1: /usr/local/freesurfer//bin/bet.fsl: /bin/imtest: not found /usr/local/freesurfer//bin/bet.fsl: 153: [: =: unexpected operator /usr/local/freesurfer//bin/bet.fsl: 231: /usr/local/freesurfer//bin/bet.fsl: /bin/bet2: not found Then I realized that the program looks for those not-found files (remove_ext, imtest, bet2) in /bin/, but actually they're all in /usr/lib/fsl/5.0/. What I did next was to copy those files from /usr/lib/fsl/5.0/ to /bin/, but then I got this error: # -- Using FSL's BET to Extract Brain-- # /usr/local/freesurfer/subjects/Retinotopy/3/Retinotopy bet.fsl /tmp/mkbrainmask_12619/in.nii /tmp/mkbrainmask_12619/brain -m -f 0.1 /bin/bet2: error while loading shared libraries: libfslvtkio.so: cannot open shared object file: No such file or directory mri_binarize --i /tmp/mkbrainmask_12619/brain_mask.nii --min .01 --o
Re: [Freesurfer] Using QDEC for 3 groups x 2 time-points
Thanks Doug. After using stage#1 of the longitudinal 2-stage model to create cross-sectional measuers of e.g. thickness change from tp1 to tp2 (e.g. thickness-pc1), I then did analyses in QDEC on these measures to see where in the brain such changes are - different from zero (within each group); and - different between groups (for every pair of groups in the current qdec table, e.g. F vs P) For thickness-pc1 it all went fine, but for area-pc1 analyses, I get this error right after starting the MonteCarlo Null-Z correction: Completed loading of analyzed data. fwhm.dat: 8.654965, rounded to 9. ERROR: CSDread(): could not open /usr/local/freesurfer/average/mult-comp-cor/fsaverage/rh/cortex/fwhm9/abs/th13/mc-z.csd. This happens regardless of the threshold used (e.g. 0.01 or 0.05) In case it's relevant, for the thickness analyses (whose correction worked fine), the fwhm.dat was 10.190419, rounded to 11. I am using FS 5.3.0 (Ubuntu). Thanks! Tudor On 17 June 2014 09:29, Douglas Greve gr...@nmr.mgh.harvard.edu wrote: It only needs to be accounted for when you compare across all 3 groups, in which case you'd have to use mri_glmfit doug On 6/17/14 12:07 AM, Tudor Popescu wrote: Hi Doug, Thanks... Presumably I'd just leave each possible pair of groups at a time in the qdec table, and delete rows corresponding to subjects of the remaining group? And then do stats on, e.g. long.thickness-rate to compare rate of change between the current pair of groups? Doesn't variability across all 3 groups somehow have to be accounted for? Tudor On 16 June 2014 20:38, Douglas Greve gr...@nmr.mgh.harvard.edu wrote: Yes, you could do each separately. doug On 6/16/14 8:10 PM, Tudor Popescu wrote: Dear FS list, I have a data set with 3 groups (2 treatments, 1 control), each with equally-spaced time-points (pre and post structural scan). I've done the 3 longitudinal pre-processing steps, and stage#1 of the two-stage model, and I would prefer to run stage#2 (cross-sectional analysis of the difference) with QDEC as opposed to with mri_glmfit. I know that QDEC is meant for 2 groups, but I see that designs with 4 or 6 groups can be analysed with QDEC (as per this https://surfer.nmr.mgh.harvard.edu/fswiki/FsgdExamples FSGD examples page) whereas designs with 3 groups cannot be. It seems to me that an even number of groups is QDEC-able while an odd number isn't, but is there any workaround so that I can still use QDEC? Perhaps if I only do pairwise comparisons one at a time, i.e. treatment1 vs control and treatment2 vs control? Many thanks! Tudor ___ 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 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] Monte Carlo correction
Hi there, I am trying to run a monte carlo correction on my average subject, using the full mri-mcsim run with 1 iterations (and about 200 participants). This is taking a long time, and the cluster I have access to has a limit of 72 hours which isn't long enough to finish processing. Is there a way to cut down on this processing time, i.e. cutting down on the iterations etc? Many thanks, Eileanoir ___ 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] Reducing Used Disk Space?
Hi Freesurfer List, Do folks have any recommendations on reducing the amount of space used by each subject? I looked a bit in the list archives but didn't see any recent tips. I had a large potential sample size (n=~750) and didn't know if I would have the estimated 375GBs processing would require. It looked as though there was potentially some space to trim (i.e., deleting some files in the mdi directory like nu.mgz, nu_noneck.mgz) once processing had completed). I wondered if anyone had a more exhaustive list (or suggestions) regarding files that could be deleted? Any help is greatly appreciated! Thanks much! Best, jamie. -- Jamie L. Hanson Postdoctoral Fellow, Laboratory of NeuroGenetics Duke University 417 Chapel Drive Duke West Campus Sociology-Psychology Building, Room 07A Durham, NC 27710 Email: jamielarshan...@gmail.com Website: http://jamiehanson.org/ ___ 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] Fwd: Improving translation of Choi striatal ROIs to original domain
Thomas, Thank you so much for this input. I tried out both the striatum and the general MNI152 template. For the striatum the match is *SO* much better. The MNI152 template also looks alright - though it's a little fuzzy. I'm pretty happy with this now and I'll definitely have more confidence in any striatum-based connectivity differences I see now. Thanks again. Paul On Thu, Jun 19, 2014 at 11:07 AM, Thomas Yeo thomas@nus.edu.sg wrote: Sorry for the slow reply. Here's a (non-ideal) suggestion: 1) Assuming you are quite happy with the freesurfer striatal parcellation in your AD subjects, then I am assuming freesurfer nonlinear registration (talairach.m3z) is working quite well. Talairach.m3z warps your subject to an internal freesurfer space (kinda like MNI305, but not quite). Let's say the freesurfer recon-all output is at something/AD_SUBJECT_FS/ 2) Run the MNI152 1mm template (the one from FSL) through recon-all. Recon-all will give you a Talairach.m3z that allows you to map the MNI152 1mm template to the internal freesurfer space. Let's say the freesurfer recon-all output is at something/MNI152_FS/ 3) Then do the following: a) Use mri_vol2vol to upsample the Choi striatal atlas which is 2mm resolution to the 1mm MNI152 template: mri_vol2vol --mov Choi_atlas.nii.gz --targ MNI152/mri/norm.mgz --regheader --o Choi_atlas1mm.nii.gz --no-save-reg --interp nearest Notice that I use norm.mgz of the MNI template rather than the original MNI template? norm.mgz is the 256 x 256 x 256 conformed version of the MNI template that recon-all puts through. b) warp the Choi_atlas1mm.nii.gz to freesurfer nonlinear volumetric space: setenv SUBJECTS_DIR something mri_vol2vol_used --mov Choi_atlas1mm.nii.gz --s MNI152_FS --targ $FREESURFER_HOME/average/mni305.cor.mgz --m3z talairach.m3z --o Choi_atlas_freesurfer_internal_space.nii.gz --interp nearest c) warp the Choi_atlas_freesurfer_internal_space.nii.gz to your subject: setenv SUBJECTS_DIR something mri_vol2vol --mov $SUBJECTS_DIR/AD_SUBJECT_FS/mri/norm.mgz --s AD_SUBJECT_FS --targ Choi_atlas_freesurfer_internal_space.nii.gz --m3z talairach.m3z --o Choi_atlas_AD_subject.nii.gz --interp nearest --inv-morph This is not optimal because of the double interpolation. You might want to use the MNI template instead of the Choi_atlas to test the above, so you can check the goodness of the warp. The final warped MNI template should hopefully look identical to your AD subject. If that works, then use the Choi_atlas. Note that mri_vol2vol does not work properly for talairach.m3z below version 5, so you should use version 5x mri_vol2vol. --Thomas On Wed, Jun 18, 2014 at 10:04 PM, Harms, Michael mha...@wustl.edu wrote: Hi, The recon-all based striatal parcellations are based on the anatomy of each particular subject, guided by a probabilistic atlas. That is inherently likely to be more accurate that just taking a set of ROIs/parcellations defined in some (non-probabilistic) atlas and warping them to each subject via an affine transformation, which is what it sounds like you are doing with the Choi ROIs. cheers, -MH -- Michael Harms, Ph.D. --- Conte Center for the Neuroscience of Mental Disorders Washington University School of Medicine Department of Psychiatry, Box 8134 660 South Euclid Ave. Tel: 314-747-6173 St. Louis, MO 63110 Email: mha...@wustl.edu From: Paul Beach pabea...@gmail.com Reply-To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Date: Wednesday, June 18, 2014 8:52 AM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Cc: Thomas Yeo thomas@nus.edu.sg, Yeo, Boon Thye Thomas -- Boon Thye Thomas Yeo ytho...@csail.mit.edu Subject: Re: [Freesurfer] Fwd: Improving translation of Choi striatal ROIs to original domain Hi Bruce, Thanks for the response. I actually got this pipeline partly from Thomas a few months back. However, I wasn't sure if anyone had suggestions perhaps for a recon-all based command for going from the MNI152 1mm template-based fit to individual subjects. The recon-all/Freesurfer inherent striatal parcellations are so well fitted to even my severe AD patients, so I was hoping I could somehow adapt this to the Choi ROIs. On Wed, Jun 18, 2014 at 8:45 AM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Paul Thomas Yeo (ccd) would be the best person to help you, but he may not be reading email for a while cheers Bruce On Wed, 18 Jun 2014, Paul Beach wrote: Hi Freesurfers, My processing stream involves moving the parcellated functional networks of Yeo and Choi to original subject domain to do connectivity analyses. While my process works very well for the Yeo networks I'm rather unsatisfied by the results of the Choi translations. I'm hoping someone has some suggestions for improving things so that the Choi ROIs map onto
Re: [Freesurfer] FLASH and MPRAGE sequences for segmentation on a GE 3.0T
the sequences specified by adni are a good resource: http://www.adni-info.org/scientists/MRIProtocols.aspx they’re known to work with freesurfer. N. On Jun 20, 2014, at 10:13 AM, Sherwood, Matt matt.sherw...@wright.edu wrote: Freesurfer, We recently gained access to a new GE Discovery MR750w 3.0T GEM MRI with a 24 channel headcoil. Because this system is located at a nearby hospital and is used clinically, we do not have a research agreement with GE in place and, therefore, cannot edit the default pulse sequences. We were wondering what scans/parameters would give us optimal segmentation (similar to MPRAGE and/or FLASH at https://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferWiki?action=AttachFiledo=gettarget=FreeSurfer_Suggested_Morphometry_Protocols.pdf). Thanks, Matthew Sherwood Medical Research Engineer Wright State Research Institute 4035 Colonel Glenn Hwy. Dayton, OH 45431 PH: 937.705.1025 FAX: 937.705.1095 EMAIL: matt.sherw...@wright.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 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] FreeSurfer Question
Hi, I was wondering if you happened to know why the origin of the rawavg.mgz image is slightly different than the origin of my original structural image that I reconed to obtain processed FreeSurfer data. Am I doing something wrong or is this expected? Is there an image that FreeSurfer creates that is has the exact dimensions and origin as my original data? Thank you in advance for all of your time and help! Best, Shazia -- *Shazia Dharssi* Columbia University Medical Center Department of Neurology Taub Institute P: (212) 305-8921 C: (319) 431-5060 ___ 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] FreeSurfer Question
Hi Shazia did you only have one input image or did you have two to motion correct and average? If only one, I thought they were exactly the same. Why do you think they are different? Bruce On Fri, 20 Jun 2014, Shazia Dharssi wrote: Hi, I was wondering if you happened to know why the origin of the rawavg.mgz image is slightly different than the origin of my original structural image that I reconed to obtain processed FreeSurfer data. Am I doing something wrong or is this expected? Is there an image that FreeSurfer creates that is has the exact dimensions and origin as my original data? Thank you in advance for all of your time and help! Best, Shazia -- Shazia Dharssi Columbia University Medical Center Department of Neurology Taub Institute P: (212) 305-8921 C: (319) 431-5060 ___ 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] MatLab Version and Hardware and Freesurfer Statistics
Dear list, Does the OS version, hardware or MatLab version (i.e., 2013a vs. 2014a) impacts in the results from the LME processing (Bernal-Rusiel et al.), employed after the Freesurfer 5.1/5.3 longitudinal pipeline? Regards, Pedro Rosa. ___ 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] Fwd: mpr2mni305 failed, see transforms/talairach_avi.log
Dear All, I am sorry to post this again. Any help will be greatly appreciated. I am struck as I am unable to run the recon-all step. Thanks Venkat -- Forwarded message -- From: Venkateswaran Rajagopalan venkateswa...@hyderabad.bits-pilani.ac.in Date: Fri, Jun 20, 2014 at 5:14 PM Subject: mpr2mni305 failed, see transforms/talairach_avi.log To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Hi All, I am getting the the following error when I run recon-all -subjid E368 -autorecon1 ERROR: mpr2mni305 failed, see transforms/talairach_avi.log Here is what talairach_avi.log says /home/administrator/Desktop/freesurfer/subjects_dir/E368/mri /usr/local/freesurfer/bin/talairach_avi --i orig_nu.mgz --xfm transforms/talairach.auto.xfm $Id: talairach_avi,v 1.9 2011/03/02 18:38:06 nicks Exp $ Linux administrator-HP-Pro-3330-MT 3.13.0-24-generic #46-Ubuntu SMP Thu Apr 10 19:08:14 UTC 2014 i686 i686 i686 GNU/Linux Fri Jun 20 17:06:38 IST 2014 mri_convert orig_nu.mgz talsrcimg.img $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from orig_nu.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) writing to talsrcimg.img... Analyze Output Matrix -1.000 0.000 0.000 129.000; 0.000 0.000 1.000 -129.000; 0.000 -1.000 0.000 122.500; 0.000 0.000 0.000 1.000; INFO: set hdr.hist.orient to -1 mpr2mni305 talsrcimg Fri Jun 20 17:06:39 IST 2014 /usr/local/freesurfer/bin/mpr2mni305 talsrcimg $Id: mpr2mni305,v 1.4 2009/06/03 16:01:38 nicks Exp $ target=711-2C_as_mni_average_305 - analyzeto4dfp talsrcimg -O0 -y - $Id: ifh2hdr.c,v 1.3 2007/05/05 10:45:03 nicks Exp $ Fri Jun 20 17:06:40 2014 Writing: talsrcimg.4dfp.hdr $Id: analyzeto4dfp.c,v 1.2 2007/05/05 00:00:06 nicks Exp $ Reading: talsrcimg.hdr header size 348 bytes hdr.dime.datatypeoffset=70value=2 hdr.dime.bitpixoffset=72value=8 hdr.hist.orientoffset=252value=-1 dimensionality 4 dimensions 256 256 256 1 Reading: talsrcimg.img Writing: talsrcimg.4dfp.img Writing: talsrcimg.4dfp.ifh ifh2hdr talsrcimg -r0to255 ori=2 - gauss_4dfp talsrcimg 1.1 - $Id: gauss_4dfp.c,v 1.3 2009/05/15 21:43:46 nicks Exp $ Reading: talsrcimg.4dfp.img Writing: talsrcimg_g11.4dfp.img image dimensions 256 256 256 padded to 288 288 288 processing volume 1$Id: ifh2hdr.c,v 1.3 2007/05/05 10:45:03 nicks Exp $ Fri Jun 20 17:06:46 2014 Writing: talsrcimg_g11.4dfp.hdr Writing: talsrcimg_g11.4dfp.ifh including: talsrcimg.4dfp.img.rec in talsrcimg_g11.4dfp.img.rec - imgreg_4dfp /usr/local/freesurfer/average/711-2C_as_mni_average_305 none talsrcimg_g11 none talsrcimg_to_711-2C_as_mni_average_305_t4 4355 - $Id: imgreg_4dfp.c,v 1.4 2010/02/27 01:41:53 nicks Exp $ imgreg_4dfp: /usr/local/freesurfer/average/711-2C_as_mni_average_305.4dfp.img read error /usr/local/freesurfer/average/711-2C_as_mni_average_305.4dfp.img 256 256 256 1 1.00 1.00 1.00 orientation T byte_order littleendian Reading image: /usr/local/freesurfer/average/711-2C_as_mni_average_305.4dfp.img dimensions: 256 256 256 mmppix: 1. -1. -1. center: 128. -129. -129. ERROR: 'imgreg_4dfp /usr/local/freesurfer/average/711-2C_as_mni_average_305 none talsrcimg_g11 none talsrcimg_to_711-2C_as_mni_average_305_t4 4355' failed! status=255 ERROR: mpr2mni305 execution aborted Any help will be greatly appreciated. Thanks Venkat ___ 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.
